diff --git a/src/managers/common/nativePythonFinder.ts b/src/managers/common/nativePythonFinder.ts
index afd5946b..5e288ef2 100644
--- a/src/managers/common/nativePythonFinder.ts
+++ b/src/managers/common/nativePythonFinder.ts
@@ -832,30 +832,38 @@ export async function getAllExtraSearchPaths(): Promise<string[]> {
     const globalSearchPaths = getGlobalSearchPaths().filter((path) => path && path.trim() !== '');
     searchDirectories.push(...globalSearchPaths);
 
-    // Get workspaceSearchPaths
-    const workspaceSearchPaths = getWorkspaceSearchPaths();
+    // Get workspaceSearchPaths — scoped per workspace folder in multi-root workspaces
+    const workspaceFolders = getWorkspaceFolders();
+    const workspaceSearchPathsPerFolder: { paths: string[]; folder?: Uri }[] = [];
+
+    if (workspaceFolders && workspaceFolders.length > 0) {
+        for (const folder of workspaceFolders) {
+            const paths = getWorkspaceSearchPaths(folder.uri);
+            workspaceSearchPathsPerFolder.push({ paths, folder: folder.uri });
+        }
+    } else {
+        // No workspace folders — fall back to unscoped call
+        workspaceSearchPathsPerFolder.push({ paths: getWorkspaceSearchPaths() });
+    }
 
-    // Resolve relative paths against workspace folders
-    for (const searchPath of workspaceSearchPaths) {
-        if (!searchPath || searchPath.trim() === '') {
-            continue;
-        }
+    // Resolve relative paths against the specific folder they came from
+    for (const { paths, folder } of workspaceSearchPathsPerFolder) {
+        for (const searchPath of paths) {
+            if (!searchPath || searchPath.trim() === '') {
+                continue;
+            }
 
-        const trimmedPath = searchPath.trim();
+            const trimmedPath = searchPath.trim();
 
-        if (isAbsolutePath(trimmedPath)) {
-            // Absolute path - use as is
-            searchDirectories.push(trimmedPath);
-        } else {
-            // Relative path - resolve against all workspace folders
-            const workspaceFolders = getWorkspaceFolders();
-            if (workspaceFolders) {
-                for (const workspaceFolder of workspaceFolders) {
-                    const resolvedPath = path.resolve(workspaceFolder.uri.fsPath, trimmedPath);
-                    searchDirectories.push(resolvedPath);
-                }
+            if (isAbsolutePath(trimmedPath)) {
+                // Absolute path - use as is
+                searchDirectories.push(trimmedPath);
+            } else if (folder) {
+                // Relative path - resolve against the specific folder it came from
+                const resolvedPath = path.resolve(folder.fsPath, trimmedPath);
+                searchDirectories.push(resolvedPath);
             } else {
-                traceWarn('No workspace folders found for relative search path:', trimmedPath);
+                traceWarn('No workspace folder for relative search path:', trimmedPath);
             }
         }
     }
@@ -897,9 +905,9 @@ export function resetWorkspaceSearchPathsGlobalWarningFlag(): void {
  * Gets the most specific workspace-level setting available for workspaceSearchPaths.
  * Supports glob patterns which are expanded by PET.
  */
-function getWorkspaceSearchPaths(): string[] {
+function getWorkspaceSearchPaths(scope?: Uri): string[] {
     try {
-        const envConfig = getConfiguration('python-envs');
+        const envConfig = getConfiguration('python-envs', scope);
         const inspection = envConfig.inspect<string[]>('workspaceSearchPaths');
 
         if (inspection?.globalValue && !workspaceSearchPathsGlobalWarningShown) {
diff --git a/src/test/managers/common/nativePythonFinder.getAllExtraSearchPaths.unit.test.ts b/src/test/managers/common/nativePythonFinder.getAllExtraSearchPaths.unit.test.ts
index 6159fdc2..617d38d7 100644
--- a/src/test/managers/common/nativePythonFinder.getAllExtraSearchPaths.unit.test.ts
+++ b/src/test/managers/common/nativePythonFinder.getAllExtraSearchPaths.unit.test.ts
@@ -1,4 +1,5 @@
 import assert from 'node:assert';
+import * as path from 'node:path';
 import * as sinon from 'sinon';
 import { Uri } from 'vscode';
 import * as logging from '../../../common/logging';
@@ -480,6 +481,133 @@ suite('getAllExtraSearchPaths Integration Tests', () => {
             assert.ok(mockTraceWarn.called, 'Should warn about missing workspace folders');
         });
 
+        test('Multi-root workspace - each folder reads its own workspaceSearchPaths', async () => {
+            // Mock → Two folders with different folder-level workspaceSearchPaths
+            const workspace1 = Uri.file('/workspace/project1');
+            const workspace2 = Uri.file('/workspace/project2');
+
+            // Create separate config objects for each folder
+            const envConfig1: MockWorkspaceConfig = {
+                get: sinon.stub(),
+                inspect: sinon.stub(),
+                update: sinon.stub(),
+            };
+            const envConfig2: MockWorkspaceConfig = {
+                get: sinon.stub(),
+                inspect: sinon.stub(),
+                update: sinon.stub(),
+            };
+
+            envConfig1.inspect.withArgs('globalSearchPaths').returns({ globalValue: [] });
+            envConfig1.inspect.withArgs('workspaceSearchPaths').returns({
+                workspaceFolderValue: ['/envs/project1'],
+            });
+
+            envConfig2.inspect.withArgs('globalSearchPaths').returns({ globalValue: [] });
+            envConfig2.inspect.withArgs('workspaceSearchPaths').returns({
+                workspaceFolderValue: ['/envs/project2'],
+            });
+
+            // Return folder-specific configs based on the scope URI passed to getConfiguration
+            mockGetConfiguration.callsFake((section: string, scope?: unknown) => {
+                if (section === 'python') {
+                    return pythonConfig;
+                }
+                if (section === 'python-envs') {
+                    if (scope && (scope as Uri).fsPath === workspace1.fsPath) {
+                        return envConfig1;
+                    }
+                    if (scope && (scope as Uri).fsPath === workspace2.fsPath) {
+                        return envConfig2;
+                    }
+                    return envConfig; // fallback for unscoped calls
+                }
+                throw new Error(`Unexpected configuration section: ${section}`);
+            });
+
+            pythonConfig.get.withArgs('venvPath').returns(undefined);
+            pythonConfig.get.withArgs('venvFolders').returns(undefined);
+            mockGetWorkspaceFolders.returns([{ uri: workspace1 }, { uri: workspace2 }]);
+
+            // Run
+            const result = await getAllExtraSearchPaths();
+
+            // Assert - each folder's workspaceSearchPaths is read independently
+            assert.ok(result.includes('/envs/project1'), 'Should include project1 env path');
+            assert.ok(result.includes('/envs/project2'), 'Should include project2 env path');
+            assert.strictEqual(result.length, 2, 'Should have exactly 2 paths (one per folder)');
+        });
+
+        test('Multi-root workspace - relative paths resolved against the correct folder', async () => {
+            // Mock → Two folders, each with a relative workspaceSearchPaths
+            const workspace1 = Uri.file('/workspace/project1');
+            const workspace2 = Uri.file('/workspace/project2');
+
+            const envConfig1: MockWorkspaceConfig = {
+                get: sinon.stub(),
+                inspect: sinon.stub(),
+                update: sinon.stub(),
+            };
+            const envConfig2: MockWorkspaceConfig = {
+                get: sinon.stub(),
+                inspect: sinon.stub(),
+                update: sinon.stub(),
+            };
+
+            envConfig1.inspect.withArgs('globalSearchPaths').returns({ globalValue: [] });
+            envConfig1.inspect.withArgs('workspaceSearchPaths').returns({
+                workspaceFolderValue: ['envs'],
+            });
+
+            envConfig2.inspect.withArgs('globalSearchPaths').returns({ globalValue: [] });
+            envConfig2.inspect.withArgs('workspaceSearchPaths').returns({
+                workspaceFolderValue: ['venvs'],
+            });
+
+            mockGetConfiguration.callsFake((section: string, scope?: unknown) => {
+                if (section === 'python') {
+                    return pythonConfig;
+                }
+                if (section === 'python-envs') {
+                    if (scope && (scope as Uri).fsPath === workspace1.fsPath) {
+                        return envConfig1;
+                    }
+                    if (scope && (scope as Uri).fsPath === workspace2.fsPath) {
+                        return envConfig2;
+                    }
+                    return envConfig;
+                }
+                throw new Error(`Unexpected configuration section: ${section}`);
+            });
+
+            pythonConfig.get.withArgs('venvPath').returns(undefined);
+            pythonConfig.get.withArgs('venvFolders').returns(undefined);
+            mockGetWorkspaceFolders.returns([{ uri: workspace1 }, { uri: workspace2 }]);
+
+            // Run
+            const result = await getAllExtraSearchPaths();
+
+            // Assert - relative paths resolved only against their own folder
+            // .replace(/\\/g, '/') mirrors the normalization getAllExtraSearchPaths() applies to all
+            // returned paths, so results always use forward slashes regardless of platform.
+            const expected1 = path.resolve(workspace1.fsPath, 'envs').replace(/\\/g, '/');
+            const expected2 = path.resolve(workspace2.fsPath, 'venvs').replace(/\\/g, '/');
+            const wrong1In2 = path.resolve(workspace2.fsPath, 'envs').replace(/\\/g, '/');
+            const wrong2In1 = path.resolve(workspace1.fsPath, 'venvs').replace(/\\/g, '/');
+
+            assert.strictEqual(result.length, 2, 'Should have exactly 2 paths (one per folder)');
+            assert.ok(result.includes(expected1), 'project1/envs should come from project1 config');
+            assert.ok(result.includes(expected2), 'project2/venvs should come from project2 config');
+            assert.ok(
+                !result.includes(wrong1In2),
+                'project1 relative path should not be resolved against project2',
+            );
+            assert.ok(
+                !result.includes(wrong2In1),
+                'project2 relative path should not be resolved against project1',
+            );
+        });
+
         test('Empty and whitespace paths are skipped', async () => {
             // Mock → Mix of valid and invalid paths
             pythonConfig.get.withArgs('venvPath').returns(undefined);