diff --git a/.github/workflows/__export-file-baseline-information.yml b/.github/workflows/__export-file-baseline-information.yml
index f157c23f75..41fb9220fd 100644
--- a/.github/workflows/__export-file-baseline-information.yml
+++ b/.github/workflows/__export-file-baseline-information.yml
@@ -125,5 +125,6 @@ jobs:
             fi
           done
     env:
+      CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS: false
       CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
       CODEQL_ACTION_TEST_MODE: true
diff --git a/lib/analyze-action-post.js b/lib/analyze-action-post.js
index d0e16267ca..a7d4804875 100644
--- a/lib/analyze-action-post.js
+++ b/lib/analyze-action-post.js
@@ -124724,6 +124724,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -124941,6 +124950,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -124950,12 +124963,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -125142,15 +125157,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/analyze-action.js b/lib/analyze-action.js
index 126b0f7ec9..c80deb0775 100644
--- a/lib/analyze-action.js
+++ b/lib/analyze-action.js
@@ -91287,6 +91287,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -93041,6 +93050,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -93050,12 +93063,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -93242,15 +93257,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
@@ -94006,10 +94012,17 @@ async function runQueries(sarifFolder, memoryFlag, threadsFlag, diffRangePackDir
       const endTimeInterpretResults = /* @__PURE__ */ new Date();
       statusReport[`interpret_results_${language}_duration_ms`] = endTimeInterpretResults.getTime() - startTimeInterpretResults.getTime();
       logger.endGroup();
-      logger.info(analysisSummary);
-      if (qualityAnalysisSummary) {
+      if (analysisSummary.trim()) {
+        logger.info(analysisSummary);
+      }
+      if (qualityAnalysisSummary?.trim()) {
         logger.info(qualityAnalysisSummary);
       }
+      if (!config.enableFileCoverageInformation) {
+        logger.info(
+          "To speed up pull request analysis, file coverage information is only enabled when analyzing the default branch and protected branches."
+        );
+      }
       if (await features.getValue("qa_telemetry_enabled" /* QaTelemetryEnabled */)) {
         const perQueryAlertCounts = getPerQueryAlertCounts(sarifFile);
         const perQueryAlertCountEventReport = {
diff --git a/lib/autobuild-action.js b/lib/autobuild-action.js
index 2e37724d49..e86b41e428 100644
--- a/lib/autobuild-action.js
+++ b/lib/autobuild-action.js
@@ -87620,6 +87620,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -88141,6 +88150,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -88150,12 +88163,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -88342,15 +88357,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/init-action-post.js b/lib/init-action-post.js
index 272e6ee6f1..5c1de14d3f 100644
--- a/lib/init-action-post.js
+++ b/lib/init-action-post.js
@@ -128119,6 +128119,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -129576,6 +129585,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -129585,12 +129598,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -129777,15 +129792,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/init-action.js b/lib/init-action.js
index 8dfb854c64..d50f4de685 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -88780,6 +88780,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -89334,7 +89343,8 @@ async function initActionState({
   features,
   repositoryProperties,
   analysisKinds,
-  logger
+  logger,
+  enableFileCoverageInformation
 }, userConfig) {
   const languages = await getLanguages(
     codeql,
@@ -89396,7 +89406,8 @@ async function initActionState({
     extraQueryExclusions: [],
     overlayDatabaseMode: "none" /* None */,
     useOverlayDatabaseCaching: false,
-    repositoryProperties
+    repositoryProperties,
+    enableFileCoverageInformation
   };
 }
 async function downloadCacheWithTime(trapCachingEnabled, codeQL, languages, logger) {
@@ -91389,6 +91400,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -91398,12 +91413,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -91590,15 +91607,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
@@ -92020,6 +92028,16 @@ function cleanupDatabaseClusterDirectory(config, logger, options = {}, rmSync2 =
     }
   }
 }
+async function getFileCoverageInformationEnabled(debugMode, repositoryNwo, features) {
+  return (
+    // Always enable file coverage information in debug mode
+    debugMode || // We're most interested in speeding up PRs, and we want to keep
+    // submitting file coverage information for the default branch since
+    // it is used to populate the status page.
+    !isAnalyzingPullRequest() || // For now, restrict this feature to the GitHub org
+    repositoryNwo.owner !== "github" || !await features.getValue("skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */)
+  );
+}
 
 // src/status-report.ts
 var os5 = __toESM(require("os"));
@@ -92626,6 +92644,7 @@ async function run(startedAt) {
       }
     }
     analysisKinds = await getAnalysisKinds(logger);
+    const debugMode = getOptionalInput("debug") === "true" || core13.isDebug();
     config = await initConfig2(features, {
       analysisKinds,
       languagesInput: getOptionalInput("languages"),
@@ -92642,7 +92661,7 @@ async function run(startedAt) {
       // - The `init` Action is passed `debug: true`.
       // - Actions step debugging is enabled (e.g. by [enabling debug logging for a rerun](https://docs.github.com/en/actions/managing-workflow-runs/re-running-workflows-and-jobs#re-running-all-the-jobs-in-a-workflow),
       //   or by setting the `ACTIONS_STEP_DEBUG` secret to `true`).
-      debugMode: getOptionalInput("debug") === "true" || core13.isDebug(),
+      debugMode,
       debugArtifactName: getOptionalInput("debug-artifact-name") || DEFAULT_DEBUG_ARTIFACT_NAME,
       debugDatabaseName: getOptionalInput("debug-database-name") || DEFAULT_DEBUG_DATABASE_NAME,
       repository: repositoryNwo,
@@ -92654,6 +92673,11 @@ async function run(startedAt) {
       apiDetails,
       features,
       repositoryProperties,
+      enableFileCoverageInformation: await getFileCoverageInformationEnabled(
+        debugMode,
+        repositoryNwo,
+        features
+      ),
       logger
     });
     await checkInstallPython311(config.languages, codeql);
diff --git a/lib/resolve-environment-action.js b/lib/resolve-environment-action.js
index 0f6546ca92..0d30268fed 100644
--- a/lib/resolve-environment-action.js
+++ b/lib/resolve-environment-action.js
@@ -87611,6 +87611,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -87834,6 +87843,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -87843,12 +87856,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -88035,15 +88050,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/setup-codeql-action.js b/lib/setup-codeql-action.js
index 914aad87da..69da4817b3 100644
--- a/lib/setup-codeql-action.js
+++ b/lib/setup-codeql-action.js
@@ -87523,6 +87523,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -89143,6 +89152,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -89152,12 +89165,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -89344,15 +89359,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/start-proxy-action-post.js b/lib/start-proxy-action-post.js
index 6d42e77685..1f423b0dba 100644
--- a/lib/start-proxy-action-post.js
+++ b/lib/start-proxy-action-post.js
@@ -124132,6 +124132,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
diff --git a/lib/start-proxy-action.js b/lib/start-proxy-action.js
index 39350b8091..a8cc0ce3c9 100644
--- a/lib/start-proxy-action.js
+++ b/lib/start-proxy-action.js
@@ -104438,6 +104438,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
diff --git a/lib/upload-lib.js b/lib/upload-lib.js
index a59f2e93f4..a41c4d41db 100644
--- a/lib/upload-lib.js
+++ b/lib/upload-lib.js
@@ -90680,6 +90680,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -91863,6 +91872,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -91872,12 +91885,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -92064,15 +92079,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/lib/upload-sarif-action-post.js b/lib/upload-sarif-action-post.js
index c7e1156f3e..3bbc115bea 100644
--- a/lib/upload-sarif-action-post.js
+++ b/lib/upload-sarif-action-post.js
@@ -124294,6 +124294,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
diff --git a/lib/upload-sarif-action.js b/lib/upload-sarif-action.js
index 1855fc99c4..ba69d872d4 100644
--- a/lib/upload-sarif-action.js
+++ b/lib/upload-sarif-action.js
@@ -90477,6 +90477,15 @@ var featureConfig = {
     legacyApi: true,
     minimumVersion: void 0
   },
+  ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: void 0
+  },
   ["upload_overlay_db_to_api" /* UploadOverlayDbToApi */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
@@ -92413,6 +92422,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -92422,12 +92435,14 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
@@ -92614,15 +92629,6 @@ ${output}`
         noStreamStdout: true
       });
     },
-    async databasePrintBaseline(databasePath) {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(config, cleanupLevel) {
       const cacheCleanupFlag = await codeQlVersionAtLeast(
         this,
diff --git a/package-lock.json b/package-lock.json
index a4792f7fdf..a5a08c4361 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -3834,9 +3834,9 @@
       }
     },
     "node_modules/caniuse-lite": {
-      "version": "1.0.30001727",
-      "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001727.tgz",
-      "integrity": "sha512-pB68nIHmbN6L/4C6MH1DokyR3bYqFwjaSs/sWDHGj4CTcFtQUQMuJftVwWkXq7mNWOybD3KhUv3oWHoGxgP14Q==",
+      "version": "1.0.30001766",
+      "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001766.tgz",
+      "integrity": "sha512-4C0lfJ0/YPjJQHagaE9x2Elb69CIqEPZeG0anQt9SIvIoOH4a4uaRl73IavyO+0qZh6MDLH//DrXThEYKHkmYA==",
       "dev": true,
       "funding": [
         {
@@ -3851,7 +3851,8 @@
           "type": "github",
           "url": "https://github.com/sponsors/ai"
         }
-      ]
+      ],
+      "license": "CC-BY-4.0"
     },
     "node_modules/cbor": {
       "version": "10.0.9",
diff --git a/pr-checks/checks/export-file-baseline-information.yml b/pr-checks/checks/export-file-baseline-information.yml
index fdc352285c..e45fc58ca3 100644
--- a/pr-checks/checks/export-file-baseline-information.yml
+++ b/pr-checks/checks/export-file-baseline-information.yml
@@ -5,6 +5,7 @@ versions: ["nightly-latest"]
 installGo: true
 installDotNet: true
 env:
+  CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS: false
   CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
 steps:
   - uses: ./../action/init
diff --git a/src/analyze.test.ts b/src/analyze.test.ts
index ceabf62baa..27fe4a6f47 100644
--- a/src/analyze.test.ts
+++ b/src/analyze.test.ts
@@ -87,7 +87,6 @@ test("status report fields", async (t) => {
           );
           return "";
         },
-        databasePrintBaseline: async () => "",
       });
 
       const config = createTestConfig({
diff --git a/src/analyze.ts b/src/analyze.ts
index dc631ba98f..bb38415047 100644
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -495,10 +495,18 @@ export async function runQueries(
         endTimeInterpretResults.getTime() - startTimeInterpretResults.getTime();
       logger.endGroup();
 
-      logger.info(analysisSummary);
-      if (qualityAnalysisSummary) {
+      if (analysisSummary.trim()) {
+        logger.info(analysisSummary);
+      }
+      if (qualityAnalysisSummary?.trim()) {
         logger.info(qualityAnalysisSummary);
       }
+      if (!config.enableFileCoverageInformation) {
+        logger.info(
+          "To speed up pull request analysis, file coverage information is only enabled when analyzing " +
+            "the default branch and protected branches.",
+        );
+      }
 
       if (await features.getValue(Feature.QaTelemetryEnabled)) {
         // Note: QA adds the `code-quality` query suite to the `queries` input,
diff --git a/src/codeql.ts b/src/codeql.ts
index f70e5ffa4f..8e7c2bfe26 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -186,10 +186,6 @@ export interface CodeQL {
     config: Config,
     features: FeatureEnablement,
   ): Promise<string>;
-  /**
-   * Run 'codeql database print-baseline'.
-   */
-  databasePrintBaseline(databasePath: string): Promise<string>;
   /**
    * Run 'codeql database export-diagnostics'
    *
@@ -493,10 +489,6 @@ export function createStubCodeQL(partialCodeql: Partial<CodeQL>): CodeQL {
       partialCodeql,
       "databaseInterpretResults",
     ),
-    databasePrintBaseline: resolveFunction(
-      partialCodeql,
-      "databasePrintBaseline",
-    ),
     databaseExportDiagnostics: resolveFunction(
       partialCodeql,
       "databaseExportDiagnostics",
@@ -628,6 +620,13 @@ async function getCodeQLForCmd(
         extraArgs.push("--overlay-base");
       }
 
+      const baselineFilesOptions = config.enableFileCoverageInformation
+        ? [
+            "--calculate-language-specific-baseline",
+            "--sublanguage-file-coverage",
+          ]
+        : ["--no-calculate-baseline"];
+
       await runCli(
         cmd,
         [
@@ -639,12 +638,14 @@ async function getCodeQLForCmd(
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"],
+            // Some user configs specify `--no-calculate-baseline` as an additional
+            // argument to `codeql database init`. Therefore ignore the baseline file
+            // options here to avoid specifying the same argument twice and erroring.
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions],
           }),
         ],
         { stdin: externalRepositoryToken },
@@ -885,15 +886,6 @@ async function getCodeQLForCmd(
         noStreamStdout: true,
       });
     },
-    async databasePrintBaseline(databasePath: string): Promise<string> {
-      const codeqlArgs = [
-        "database",
-        "print-baseline",
-        ...getExtraOptionsFromEnv(["database", "print-baseline"]),
-        databasePath,
-      ];
-      return await runCli(cmd, codeqlArgs);
-    },
     async databaseCleanupCluster(
       config: Config,
       cleanupLevel: CleanupLevel,
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index 337eb85c59..276a7a344b 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -89,6 +89,7 @@ function createTestInitConfigInputs(
       },
       features: createFeatures([]),
       repositoryProperties: {},
+      enableFileCoverageInformation: true,
       logger: getRunnerLogger(true),
     } satisfies configUtils.InitConfigInputs,
     overrides,
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 772c187b83..a010418993 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -214,6 +214,11 @@ export interface Config {
    * A partial mapping from repository properties that affect us to their values.
    */
   repositoryProperties: RepositoryProperties;
+
+  /**
+   * Whether to enable file coverage information.
+   */
+  enableFileCoverageInformation: boolean;
 }
 
 async function getSupportedLanguageMap(
@@ -433,6 +438,7 @@ export interface InitConfigInputs {
   apiDetails: api.GitHubApiCombinedDetails;
   features: FeatureEnablement;
   repositoryProperties: RepositoryProperties;
+  enableFileCoverageInformation: boolean;
   analysisKinds: AnalysisKind[];
   logger: Logger;
 }
@@ -462,6 +468,7 @@ export async function initActionState(
     repositoryProperties,
     analysisKinds,
     logger,
+    enableFileCoverageInformation,
   }: InitConfigInputs,
   userConfig: UserConfig,
 ): Promise<Config> {
@@ -542,6 +549,7 @@ export async function initActionState(
     overlayDatabaseMode: OverlayDatabaseMode.None,
     useOverlayDatabaseCaching: false,
     repositoryProperties,
+    enableFileCoverageInformation,
   };
 }
 
diff --git a/src/feature-flags.ts b/src/feature-flags.ts
index 7ad9ecfa48..8de68a28d7 100644
--- a/src/feature-flags.ts
+++ b/src/feature-flags.ts
@@ -70,6 +70,8 @@ export enum Feature {
   OverlayAnalysisSwift = "overlay_analysis_swift",
   PythonDefaultIsToNotExtractStdlib = "python_default_is_to_not_extract_stdlib",
   QaTelemetryEnabled = "qa_telemetry_enabled",
+  /** Note that this currently only disables baseline file coverage information. */
+  SkipFileCoverageOnPrs = "skip_file_coverage_on_prs",
   UploadOverlayDbToApi = "upload_overlay_db_to_api",
   UseRepositoryProperties = "use_repository_properties",
   ValidateDbConfig = "validate_db_config",
@@ -286,6 +288,15 @@ export const featureConfig = {
     legacyApi: true,
     minimumVersion: undefined,
   },
+  [Feature.SkipFileCoverageOnPrs]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
+    // For testing, this is not behind a CLI version check yet. However
+    // before rolling this out externally, we should set a minimum version here
+    // since current versions of the CodeQL CLI will log if baseline information
+    // cannot be found when interpreting results.
+    minimumVersion: undefined,
+  },
   [Feature.UploadOverlayDbToApi]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
diff --git a/src/init-action.ts b/src/init-action.ts
index 8b6c200a05..0d92f46ef9 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -42,6 +42,7 @@ import {
   checkInstallPython311,
   checkPacksForOverlayCompatibility,
   cleanupDatabaseClusterDirectory,
+  getFileCoverageInformationEnabled,
   initCodeQL,
   initConfig,
   runDatabaseInitCluster,
@@ -334,6 +335,7 @@ async function run(startedAt: Date) {
     }
 
     analysisKinds = await getAnalysisKinds(logger);
+    const debugMode = getOptionalInput("debug") === "true" || core.isDebug();
     config = await initConfig(features, {
       analysisKinds,
       languagesInput: getOptionalInput("languages"),
@@ -350,7 +352,7 @@ async function run(startedAt: Date) {
       // - The `init` Action is passed `debug: true`.
       // - Actions step debugging is enabled (e.g. by [enabling debug logging for a rerun](https://docs.github.com/en/actions/managing-workflow-runs/re-running-workflows-and-jobs#re-running-all-the-jobs-in-a-workflow),
       //   or by setting the `ACTIONS_STEP_DEBUG` secret to `true`).
-      debugMode: getOptionalInput("debug") === "true" || core.isDebug(),
+      debugMode,
       debugArtifactName:
         getOptionalInput("debug-artifact-name") || DEFAULT_DEBUG_ARTIFACT_NAME,
       debugDatabaseName:
@@ -364,6 +366,11 @@ async function run(startedAt: Date) {
       apiDetails,
       features,
       repositoryProperties,
+      enableFileCoverageInformation: await getFileCoverageInformationEnabled(
+        debugMode,
+        repositoryNwo,
+        features,
+      ),
       logger,
     });
 
diff --git a/src/init.test.ts b/src/init.test.ts
index 6640e081f3..8106a78f9a 100644
--- a/src/init.test.ts
+++ b/src/init.test.ts
@@ -2,14 +2,20 @@ import * as fs from "fs";
 import path from "path";
 
 import test, { ExecutionContext } from "ava";
+import * as sinon from "sinon";
 
+import * as actionsUtil from "./actions-util";
 import { createStubCodeQL } from "./codeql";
+import { Feature } from "./feature-flags";
 import {
   checkPacksForOverlayCompatibility,
   cleanupDatabaseClusterDirectory,
+  getFileCoverageInformationEnabled,
 } from "./init";
 import { KnownLanguage } from "./languages";
+import { parseRepositoryNwo } from "./repository";
 import {
+  createFeatures,
   LoggedMessage,
   createTestConfig,
   getRecordingLogger,
@@ -442,3 +448,61 @@ test(
     expectedResult: true,
   },
 );
+
+test("file coverage information enabled when debugMode is true", async (t) => {
+  t.true(
+    await getFileCoverageInformationEnabled(
+      true, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
+
+test("file coverage information enabled when not analyzing a pull request", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(false);
+
+  t.true(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
+
+test("file coverage information enabled when owner is not 'github'", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
+
+  t.true(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("other-org/some-repo"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
+
+test("file coverage information enabled when feature flag is not enabled", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
+
+  t.true(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([]),
+    ),
+  );
+});
+
+test("file coverage information disabled when all conditions for skipping are met", async (t) => {
+  sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
+
+  t.false(
+    await getFileCoverageInformationEnabled(
+      false, // debugMode
+      parseRepositoryNwo("github/codeql-action"),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+    ),
+  );
+});
diff --git a/src/init.ts b/src/init.ts
index b399ef8d9d..a5c8e9ec02 100644
--- a/src/init.ts
+++ b/src/init.ts
@@ -5,13 +5,22 @@ import * as toolrunner from "@actions/exec/lib/toolrunner";
 import * as io from "@actions/io";
 import * as yaml from "js-yaml";
 
-import { getOptionalInput, isSelfHostedRunner } from "./actions-util";
+import {
+  getOptionalInput,
+  isAnalyzingPullRequest,
+  isSelfHostedRunner,
+} from "./actions-util";
 import { GitHubApiDetails } from "./api-client";
 import { CodeQL, setupCodeQL } from "./codeql";
 import * as configUtils from "./config-utils";
-import { CodeQLDefaultVersionInfo, FeatureEnablement } from "./feature-flags";
+import {
+  CodeQLDefaultVersionInfo,
+  Feature,
+  FeatureEnablement,
+} from "./feature-flags";
 import { KnownLanguage, Language } from "./languages";
 import { Logger, withGroupAsync } from "./logging";
+import { RepositoryNwo } from "./repository";
 import { ToolsSource } from "./setup-codeql";
 import { ZstdAvailability } from "./tar";
 import { ToolsDownloadStatusReport } from "./tools-download";
@@ -288,3 +297,21 @@ export function cleanupDatabaseClusterDirectory(
     }
   }
 }
+
+export async function getFileCoverageInformationEnabled(
+  debugMode: boolean,
+  repositoryNwo: RepositoryNwo,
+  features: FeatureEnablement,
+): Promise<boolean> {
+  return (
+    // Always enable file coverage information in debug mode
+    debugMode ||
+    // We're most interested in speeding up PRs, and we want to keep
+    // submitting file coverage information for the default branch since
+    // it is used to populate the status page.
+    !isAnalyzingPullRequest() ||
+    // For now, restrict this feature to the GitHub org
+    repositoryNwo.owner !== "github" ||
+    !(await features.getValue(Feature.SkipFileCoverageOnPrs))
+  );
+}
diff --git a/src/testing-utils.ts b/src/testing-utils.ts
index 66a6c25fb7..a2b8a5a941 100644
--- a/src/testing-utils.ts
+++ b/src/testing-utils.ts
@@ -408,6 +408,7 @@ export function createTestConfig(overrides: Partial<Config>): Config {
       overlayDatabaseMode: OverlayDatabaseMode.None,
       useOverlayDatabaseCaching: false,
       repositoryProperties: {},
+      enableFileCoverageInformation: true,
     } satisfies Config,
     overrides,
   );