diff --git a/.changeset/little-pants-call.md b/.changeset/little-pants-call.md
new file mode 100644
index 00000000..aa3cafee
--- /dev/null
+++ b/.changeset/little-pants-call.md
@@ -0,0 +1,7 @@
+---
+'@powersync/service-module-mongodb': patch
+'@powersync/service-core': patch
+'@powersync/service-image': patch
+---
+
+[MongoDB] Optimize change stream filters to avoid PSYNC_S1345 timeouts
diff --git a/modules/module-mongodb/src/replication/ChangeStream.ts b/modules/module-mongodb/src/replication/ChangeStream.ts
index 62d3cda1..0fa47f8a 100644
--- a/modules/module-mongodb/src/replication/ChangeStream.ts
+++ b/modules/module-mongodb/src/replication/ChangeStream.ts
@@ -110,6 +110,8 @@ export class ChangeStream {
 
   private snapshotChunkLength: number;
 
+  private changeStreamTimeout: number;
+
   constructor(options: ChangeStreamOptions) {
     this.storage = options.storage;
     this.metrics = options.metrics;
@@ -122,6 +124,9 @@ export class ChangeStream {
     this.sync_rules = options.storage.getParsedSyncRules({
       defaultSchema: this.defaultDb.databaseName
     });
+    // The change stream aggregation command should timeout before the socket times out,
+    // so we use 90% of the socket timeout value.
+    this.changeStreamTimeout = Math.ceil(this.client.options.socketTimeoutMS * 0.9);
 
     this.abort_signal = options.abort_signal;
     this.abort_signal.addEventListener(
@@ -411,8 +416,10 @@ export class ChangeStream {
   private getSourceNamespaceFilters(): { $match: any; multipleDatabases: boolean } {
     const sourceTables = this.sync_rules.getSourceTables();
 
-    let $inFilters: any[] = [{ db: this.defaultDb.databaseName, coll: CHECKPOINTS_COLLECTION }];
-    let $refilters: any[] = [];
+    let $inFilters: { db: string; coll: string }[] = [
+      { db: this.defaultDb.databaseName, coll: CHECKPOINTS_COLLECTION }
+    ];
+    let $refilters: { 'ns.db': string; 'ns.coll': RegExp }[] = [];
     let multipleDatabases = false;
     for (let tablePattern of sourceTables) {
       if (tablePattern.connectionTag != this.connections.connectionTag) {
@@ -435,10 +442,26 @@ export class ChangeStream {
         });
       }
     }
+
+    // When we have a large number of collections, the performance of the pipeline
+    // depends a lot on how the filters here are specified.
+    // Currently, only the multipleDatabases == false case is optimized, and the
+    // wildcard matching version is not tested (but we assume that will be more
+    // limited in the number of them).
+    // Specifically, the `ns: {$in: [...]}` version can lead to PSYNC_S1345 timeouts in
+    // some cases when we have a large number of collections.
+    // For details, see:
+    // https://github.com/powersync-ja/powersync-service/pull/417
+    // https://jira.mongodb.org/browse/SERVER-114532
+    const nsFilter = multipleDatabases
+      ? // cluster-level: filter on the entire namespace
+        { ns: { $in: $inFilters } }
+      : // collection-level: filter on coll only
+        { 'ns.coll': { $in: $inFilters.map((ns) => ns.coll) } };
     if ($refilters.length > 0) {
-      return { $match: { $or: [{ ns: { $in: $inFilters } }, ...$refilters] }, multipleDatabases };
+      return { $match: { $or: [nsFilter, ...$refilters] }, multipleDatabases };
     }
-    return { $match: { ns: { $in: $inFilters } }, multipleDatabases };
+    return { $match: nsFilter, multipleDatabases };
   }
 
   static *getQueryData(results: Iterable<DatabaseInputRow>): Generator<SqliteInputRow> {
@@ -747,11 +770,11 @@ export class ChangeStream {
     } else {
       fullDocument = 'updateLookup';
     }
-
     const streamOptions: mongo.ChangeStreamOptions = {
       showExpandedEvents: true,
       maxAwaitTimeMS: options.maxAwaitTimeMs ?? this.maxAwaitTimeMS,
-      fullDocument: fullDocument
+      fullDocument: fullDocument,
+      maxTimeMS: this.changeStreamTimeout
     };
 
     /**
@@ -1103,6 +1126,10 @@ function mapChangeStreamError(e: any) {
     // This typically has an unhelpful message like "connection 2 to 159.41.94.47:27017 timed out".
     // We wrap the error to make it more useful.
     throw new DatabaseConnectionError(ErrorCode.PSYNC_S1345, `Timeout while reading MongoDB ChangeStream`, e);
+  } else if (isMongoServerError(e) && e.codeName == 'MaxTimeMSExpired') {
+    // maxTimeMS was reached. Example message:
+    // MongoServerError: Executor error during aggregate command on namespace: powersync_test_data.$cmd.aggregate :: caused by :: operation exceeded time limit
+    throw new DatabaseConnectionError(ErrorCode.PSYNC_S1345, `Timeout while reading MongoDB ChangeStream`, e);
   } else if (
     isMongoServerError(e) &&
     e.codeName == 'NoMatchingDocument' &&