diff --git a/src/services/code-index/processors/file-watcher.ts b/src/services/code-index/processors/file-watcher.ts
index 3f04a73072..c0bacc621d 100644
--- a/src/services/code-index/processors/file-watcher.ts
+++ b/src/services/code-index/processors/file-watcher.ts
@@ -525,7 +525,7 @@ export class FileWatcher implements IFileWatcher {
 			// Check if file should be ignored
 			const relativeFilePath = generateRelativeFilePath(filePath, this.workspacePath)
 			if (
-				!this.ignoreController.validateAccess(filePath) ||
+				!this.ignoreController.validateAccess(relativeFilePath) ||
 				(this.ignoreInstance && this.ignoreInstance.ignores(relativeFilePath))
 			) {
 				return {
diff --git a/src/services/code-index/processors/scanner.ts b/src/services/code-index/processors/scanner.ts
index 3da6fc364f..aab95d7511 100644
--- a/src/services/code-index/processors/scanner.ts
+++ b/src/services/code-index/processors/scanner.ts
@@ -86,7 +86,9 @@ export class DirectoryScanner implements IDirectoryScanner {
 		// IMPORTANT: do not create a file watcher here (scan is short-lived).
 		let allowedPaths: string[]
 		{
-			const ignoreController = new RooIgnoreController(directoryPath, { watch: false })
+			// Root the controller at the effective workspace to ensure `.rooignore` checks
+			// are consistent with other workspace-relative filtering.
+			const ignoreController = new RooIgnoreController(scanWorkspace, { watch: false })
 			try {
 				await ignoreController.initialize()
 				// Filter paths using .rooignore