diff --git a/src/core/ignore/RooIgnoreController.ts b/src/core/ignore/RooIgnoreController.ts
index fda6c37175..90654983b9 100644
--- a/src/core/ignore/RooIgnoreController.ts
+++ b/src/core/ignore/RooIgnoreController.ts
@@ -60,7 +60,7 @@ export class RooIgnoreController {
 	/**
 	 * Load custom patterns from .rooignore if it exists
 	 */
-	private async loadRooIgnore(): Promise<void> {
+	public async loadRooIgnore(): Promise<void> {
 		try {
 			// Reset ignore instance to prevent duplicate patterns
 			this.ignoreInstance = ignore()
@@ -183,7 +183,7 @@ export class RooIgnoreController {
 	 * Clean up resources when the controller is no longer needed
 	 */
 	dispose(): void {
-		this.disposables.forEach((d) => d.dispose())
+		this.disposables.forEach((d) => d?.dispose?.())
 		this.disposables = []
 	}
 
diff --git a/src/services/code-index/__tests__/ignore-integration.spec.ts b/src/services/code-index/__tests__/ignore-integration.spec.ts
new file mode 100644
index 0000000000..f63e0de4f2
--- /dev/null
+++ b/src/services/code-index/__tests__/ignore-integration.spec.ts
@@ -0,0 +1,492 @@
+import { describe, it, expect, vi, beforeEach, afterEach } from "vitest"
+import { CodeIndexManager } from "../manager"
+import { CodeIndexServiceFactory } from "../service-factory"
+import type { MockedClass } from "vitest"
+import fs from "fs/promises"
+import path from "path"
+
+// Mock vscode module
+vi.mock("vscode", () => ({
+	workspace: {
+		workspaceFolders: [
+			{
+				uri: { fsPath: "/test/workspace" },
+				name: "test",
+				index: 0,
+			},
+		],
+		createFileSystemWatcher: vi.fn(() => ({
+			onDidCreate: vi.fn(),
+			onDidChange: vi.fn(),
+			onDidDelete: vi.fn(),
+			dispose: vi.fn(),
+		})),
+	},
+	RelativePattern: vi.fn().mockImplementation((base, pattern) => ({
+		base,
+		pattern,
+	})),
+}))
+
+// Mock path utilities
+vi.mock("../../../utils/path", () => ({
+	getWorkspacePath: vi.fn(() => "/test/workspace"),
+}))
+
+// Mock fs operations
+vi.mock("fs/promises")
+const mockFs = fs as any
+
+// Mock file existence check
+vi.mock("../../../utils/fs", () => ({
+	fileExistsAtPath: vi.fn(),
+}))
+
+// Mock glob utilities
+vi.mock("../../glob/list-files", () => ({
+	findGitignoreFiles: vi.fn(),
+}))
+
+// Mock state manager
+vi.mock("../state-manager", () => ({
+	CodeIndexStateManager: vi.fn().mockImplementation(() => ({
+		onProgressUpdate: vi.fn(),
+		getCurrentStatus: vi.fn(),
+		dispose: vi.fn(),
+		setSystemState: vi.fn(),
+	})),
+}))
+
+// Mock telemetry
+vi.mock("@roo-code/telemetry", () => ({
+	TelemetryService: {
+		instance: {
+			captureEvent: vi.fn(),
+		},
+	},
+}))
+
+// Mock service factory
+vi.mock("../service-factory")
+const MockedCodeIndexServiceFactory = CodeIndexServiceFactory as MockedClass<typeof CodeIndexServiceFactory>
+
+describe("CodeIndexManager - Ignore Integration Tests", () => {
+	let mockContext: any
+	let manager: CodeIndexManager
+
+	beforeEach(() => {
+		// Clear all instances before each test
+		CodeIndexManager.disposeAll()
+
+		mockContext = {
+			subscriptions: [],
+			workspaceState: {} as any,
+			globalState: {} as any,
+			extensionUri: {} as any,
+			extensionPath: "/test/extension",
+			asAbsolutePath: vi.fn(),
+			storageUri: {} as any,
+			storagePath: "/test/storage",
+			globalStorageUri: {} as any,
+			globalStoragePath: "/test/global-storage",
+			logUri: {} as any,
+			logPath: "/test/log",
+			extensionMode: 3, // vscode.ExtensionMode.Test
+			secrets: {} as any,
+			environmentVariableCollection: {} as any,
+			extension: {} as any,
+			languageModelAccessInformation: {} as any,
+		}
+
+		manager = CodeIndexManager.getInstance(mockContext)!
+	})
+
+	afterEach(() => {
+		CodeIndexManager.disposeAll()
+		vi.clearAllMocks()
+	})
+
+	describe("gitignore integration", () => {
+		it("should load and apply .gitignore patterns during service recreation", async () => {
+			// Mock .gitignore file discovery and content
+			const { findGitignoreFiles } = await import("../../glob/list-files")
+			const mockFindGitignoreFiles = findGitignoreFiles as any
+			mockFindGitignoreFiles.mockResolvedValue(["/test/workspace/.gitignore"])
+
+			// Mock .gitignore content
+			mockFs.readFile.mockResolvedValue("node_modules/\n*.log\n.env")
+
+			// Mock config manager
+			const mockConfigManager = {
+				loadConfiguration: vi.fn().mockResolvedValue({ requiresRestart: false }),
+				isFeatureConfigured: true,
+				isFeatureEnabled: true,
+				getConfig: vi.fn().mockReturnValue({
+					isConfigured: true,
+					embedderProvider: "openai",
+					modelId: "text-embedding-3-small",
+					openAiOptions: { openAiNativeApiKey: "test-key" },
+					qdrantUrl: "http://localhost:6333",
+					qdrantApiKey: "test-key",
+					searchMinScore: 0.4,
+				}),
+			}
+			;(manager as any)._configManager = mockConfigManager
+
+			// Mock cache manager
+			const mockCacheManager = {
+				initialize: vi.fn(),
+				clearCacheFile: vi.fn(),
+			}
+			;(manager as any)._cacheManager = mockCacheManager
+
+			// Mock service factory
+			const mockServiceFactoryInstance = {
+				createServices: vi.fn().mockReturnValue({
+					embedder: { embedderInfo: { name: "openai" } },
+					vectorStore: {},
+					scanner: {},
+					fileWatcher: {
+						onDidStartBatchProcessing: vi.fn(),
+						onBatchProgressUpdate: vi.fn(),
+						watch: vi.fn(),
+						stopWatcher: vi.fn(),
+						dispose: vi.fn(),
+					},
+				}),
+				validateEmbedder: vi.fn().mockResolvedValue({ valid: true }),
+			}
+			MockedCodeIndexServiceFactory.mockImplementation(() => mockServiceFactoryInstance as any)
+
+			// Act - call _recreateServices which should load .gitignore
+			await (manager as any)._recreateServices()
+
+			// Assert
+			expect(mockFindGitignoreFiles).toHaveBeenCalledWith("/test/workspace")
+			expect(mockFs.readFile).toHaveBeenCalledWith("/test/workspace/.gitignore", "utf8")
+			expect(mockServiceFactoryInstance.createServices).toHaveBeenCalled()
+
+			// Verify that the ignore instance was passed to createServices with .gitignore patterns
+			const createServicesCall = mockServiceFactoryInstance.createServices.mock.calls[0]
+			const ignoreInstance = createServicesCall[2] // Third parameter is the ignore instance
+
+			// Test that the ignore instance has the expected patterns
+			expect(ignoreInstance.ignores("node_modules/package.json")).toBe(true)
+			expect(ignoreInstance.ignores("debug.log")).toBe(true)
+			expect(ignoreInstance.ignores(".env")).toBe(true)
+			expect(ignoreInstance.ignores(".gitignore")).toBe(true) // Should always ignore .gitignore files
+			expect(ignoreInstance.ignores("src/main.ts")).toBe(false)
+		})
+
+		it("should handle missing .gitignore files gracefully", async () => {
+			// Mock no .gitignore files found
+			const { findGitignoreFiles } = await import("../../glob/list-files")
+			const mockFindGitignoreFiles = findGitignoreFiles as any
+			mockFindGitignoreFiles.mockResolvedValue([])
+
+			// Mock config manager
+			const mockConfigManager = {
+				loadConfiguration: vi.fn().mockResolvedValue({ requiresRestart: false }),
+				isFeatureConfigured: true,
+				isFeatureEnabled: true,
+				getConfig: vi.fn().mockReturnValue({
+					isConfigured: true,
+					embedderProvider: "openai",
+					modelId: "text-embedding-3-small",
+					openAiOptions: { openAiNativeApiKey: "test-key" },
+					qdrantUrl: "http://localhost:6333",
+					qdrantApiKey: "test-key",
+					searchMinScore: 0.4,
+				}),
+			}
+			;(manager as any)._configManager = mockConfigManager
+
+			// Mock cache manager
+			const mockCacheManager = {
+				initialize: vi.fn(),
+				clearCacheFile: vi.fn(),
+			}
+			;(manager as any)._cacheManager = mockCacheManager
+
+			// Mock service factory
+			const mockServiceFactoryInstance = {
+				createServices: vi.fn().mockReturnValue({
+					embedder: { embedderInfo: { name: "openai" } },
+					vectorStore: {},
+					scanner: {},
+					fileWatcher: {
+						onDidStartBatchProcessing: vi.fn(),
+						onBatchProgressUpdate: vi.fn(),
+						watch: vi.fn(),
+						stopWatcher: vi.fn(),
+						dispose: vi.fn(),
+					},
+				}),
+				validateEmbedder: vi.fn().mockResolvedValue({ valid: true }),
+			}
+			MockedCodeIndexServiceFactory.mockImplementation(() => mockServiceFactoryInstance as any)
+
+			// Act - should not throw even with no .gitignore files
+			await expect((manager as any)._recreateServices()).resolves.not.toThrow()
+
+			// Assert
+			expect(mockFindGitignoreFiles).toHaveBeenCalledWith("/test/workspace")
+			expect(mockFs.readFile).not.toHaveBeenCalled()
+			expect(mockServiceFactoryInstance.createServices).toHaveBeenCalled()
+
+			// Verify that an ignore instance was still created (even if empty)
+			const createServicesCall = mockServiceFactoryInstance.createServices.mock.calls[0]
+			const ignoreInstance = createServicesCall[2]
+
+			// Should still ignore .gitignore files themselves
+			expect(ignoreInstance.ignores(".gitignore")).toBe(true)
+			expect(ignoreInstance.ignores("src/main.ts")).toBe(false)
+		})
+	})
+
+	describe("rooignore integration", () => {
+		it("should preserve RooIgnoreController instance across service recreations", async () => {
+			// Mock file existence check
+			const { fileExistsAtPath } = await import("../../../utils/fs")
+			const mockFileExistsAtPath = fileExistsAtPath as any
+			mockFileExistsAtPath.mockResolvedValue(true)
+
+			// Mock .rooignore content
+			mockFs.readFile.mockResolvedValue("*.secret\ntemp/")
+
+			// Mock config manager
+			const mockConfigManager = {
+				loadConfiguration: vi.fn().mockResolvedValue({ requiresRestart: false }),
+				isFeatureConfigured: true,
+				isFeatureEnabled: true,
+				getConfig: vi.fn().mockReturnValue({
+					isConfigured: true,
+					embedderProvider: "openai",
+					modelId: "text-embedding-3-small",
+					openAiOptions: { openAiNativeApiKey: "test-key" },
+					qdrantUrl: "http://localhost:6333",
+					qdrantApiKey: "test-key",
+					searchMinScore: 0.4,
+				}),
+			}
+			;(manager as any)._configManager = mockConfigManager
+
+			// Mock cache manager
+			const mockCacheManager = {
+				initialize: vi.fn(),
+				clearCacheFile: vi.fn(),
+			}
+			;(manager as any)._cacheManager = mockCacheManager
+
+			// Mock .gitignore discovery
+			const { findGitignoreFiles } = await import("../../glob/list-files")
+			const mockFindGitignoreFiles = findGitignoreFiles as any
+			mockFindGitignoreFiles.mockResolvedValue([])
+
+			// Mock service factory
+			const mockServiceFactoryInstance = {
+				createServices: vi.fn().mockReturnValue({
+					embedder: { embedderInfo: { name: "openai" } },
+					vectorStore: {},
+					scanner: {},
+					fileWatcher: {
+						onDidStartBatchProcessing: vi.fn(),
+						onBatchProgressUpdate: vi.fn(),
+						watch: vi.fn(),
+						stopWatcher: vi.fn(),
+						dispose: vi.fn(),
+					},
+				}),
+				validateEmbedder: vi.fn().mockResolvedValue({ valid: true }),
+			}
+			MockedCodeIndexServiceFactory.mockImplementation(() => mockServiceFactoryInstance as any)
+
+			// Act - call _recreateServices twice to simulate "Clear Index Data" scenario
+			await (manager as any)._recreateServices()
+			const firstRooIgnoreController = (manager as any)._rooIgnoreController
+
+			await (manager as any)._recreateServices()
+			const secondRooIgnoreController = (manager as any)._rooIgnoreController
+
+			// Assert - should be the same instance (preserved across recreations)
+			expect(firstRooIgnoreController).toBe(secondRooIgnoreController)
+			expect(firstRooIgnoreController).toBeDefined()
+
+			// Verify that loadRooIgnore was called on both recreations
+			expect(mockFileExistsAtPath).toHaveBeenCalledWith("/test/workspace/.rooignore")
+			expect(mockFs.readFile).toHaveBeenCalledWith("/test/workspace/.rooignore", "utf8")
+
+			// Verify that the RooIgnoreController was passed to createServices
+			expect(mockServiceFactoryInstance.createServices).toHaveBeenCalledTimes(2)
+			const firstCall = mockServiceFactoryInstance.createServices.mock.calls[0]
+			const secondCall = mockServiceFactoryInstance.createServices.mock.calls[1]
+
+			// Fourth parameter should be the RooIgnoreController
+			expect(firstCall[3]).toBe(firstRooIgnoreController)
+			expect(secondCall[3]).toBe(secondRooIgnoreController)
+			expect(firstCall[3]).toBe(secondCall[3]) // Same instance
+		})
+
+		it("should reload .rooignore patterns on each service recreation", async () => {
+			// Mock file existence check
+			const { fileExistsAtPath } = await import("../../../utils/fs")
+			const mockFileExistsAtPath = fileExistsAtPath as any
+			mockFileExistsAtPath.mockResolvedValue(true)
+
+			// Mock .rooignore content
+			mockFs.readFile.mockResolvedValue("*.secret\ntemp/")
+
+			// Create a spy on the RooIgnoreController's loadRooIgnore method
+			const mockLoadRooIgnore = vi.fn().mockResolvedValue(undefined)
+
+			// Mock config manager
+			const mockConfigManager = {
+				loadConfiguration: vi.fn().mockResolvedValue({ requiresRestart: false }),
+				isFeatureConfigured: true,
+				isFeatureEnabled: true,
+				getConfig: vi.fn().mockReturnValue({
+					isConfigured: true,
+					embedderProvider: "openai",
+					modelId: "text-embedding-3-small",
+					openAiOptions: { openAiNativeApiKey: "test-key" },
+					qdrantUrl: "http://localhost:6333",
+					qdrantApiKey: "test-key",
+					searchMinScore: 0.4,
+				}),
+			}
+			;(manager as any)._configManager = mockConfigManager
+
+			// Mock cache manager
+			const mockCacheManager = {
+				initialize: vi.fn(),
+				clearCacheFile: vi.fn(),
+			}
+			;(manager as any)._cacheManager = mockCacheManager
+
+			// Mock .gitignore discovery
+			const { findGitignoreFiles } = await import("../../glob/list-files")
+			const mockFindGitignoreFiles = findGitignoreFiles as any
+			mockFindGitignoreFiles.mockResolvedValue([])
+
+			// Pre-set a mock RooIgnoreController to test reloading
+			;(manager as any)._rooIgnoreController = {
+				loadRooIgnore: mockLoadRooIgnore,
+				dispose: vi.fn(),
+			}
+
+			// Mock service factory
+			const mockServiceFactoryInstance = {
+				createServices: vi.fn().mockReturnValue({
+					embedder: { embedderInfo: { name: "openai" } },
+					vectorStore: {},
+					scanner: {},
+					fileWatcher: {
+						onDidStartBatchProcessing: vi.fn(),
+						onBatchProgressUpdate: vi.fn(),
+						watch: vi.fn(),
+						stopWatcher: vi.fn(),
+						dispose: vi.fn(),
+					},
+				}),
+				validateEmbedder: vi.fn().mockResolvedValue({ valid: true }),
+			}
+			MockedCodeIndexServiceFactory.mockImplementation(() => mockServiceFactoryInstance as any)
+
+			// Act - call _recreateServices
+			await (manager as any)._recreateServices()
+
+			// Assert - loadRooIgnore should have been called to reload patterns
+			expect(mockLoadRooIgnore).toHaveBeenCalledTimes(1)
+		})
+	})
+
+	describe("integration with service factory", () => {
+		it("should pass both gitignore and rooignore controllers to service factory", async () => {
+			// Mock .gitignore discovery
+			const { findGitignoreFiles } = await import("../../glob/list-files")
+			const mockFindGitignoreFiles = findGitignoreFiles as any
+			mockFindGitignoreFiles.mockResolvedValue(["/test/workspace/.gitignore"])
+
+			// Mock .gitignore content
+			mockFs.readFile.mockImplementation((filePath: string) => {
+				if (filePath === "/test/workspace/.gitignore") {
+					return Promise.resolve("node_modules/\n*.log")
+				}
+				if (filePath === "/test/workspace/.rooignore") {
+					return Promise.resolve("*.secret\ntemp/")
+				}
+				return Promise.reject(new Error("File not found"))
+			})
+
+			// Mock file existence for .rooignore
+			const { fileExistsAtPath } = await import("../../../utils/fs")
+			const mockFileExistsAtPath = fileExistsAtPath as any
+			mockFileExistsAtPath.mockResolvedValue(true)
+
+			// Mock config manager
+			const mockConfigManager = {
+				loadConfiguration: vi.fn().mockResolvedValue({ requiresRestart: false }),
+				isFeatureConfigured: true,
+				isFeatureEnabled: true,
+				getConfig: vi.fn().mockReturnValue({
+					isConfigured: true,
+					embedderProvider: "openai",
+					modelId: "text-embedding-3-small",
+					openAiOptions: { openAiNativeApiKey: "test-key" },
+					qdrantUrl: "http://localhost:6333",
+					qdrantApiKey: "test-key",
+					searchMinScore: 0.4,
+				}),
+			}
+			;(manager as any)._configManager = mockConfigManager
+
+			// Mock cache manager
+			const mockCacheManager = {
+				initialize: vi.fn(),
+				clearCacheFile: vi.fn(),
+			}
+			;(manager as any)._cacheManager = mockCacheManager
+
+			// Mock service factory
+			const mockServiceFactoryInstance = {
+				createServices: vi.fn().mockReturnValue({
+					embedder: { embedderInfo: { name: "openai" } },
+					vectorStore: {},
+					scanner: {},
+					fileWatcher: {
+						onDidStartBatchProcessing: vi.fn(),
+						onBatchProgressUpdate: vi.fn(),
+						watch: vi.fn(),
+						stopWatcher: vi.fn(),
+						dispose: vi.fn(),
+					},
+				}),
+				validateEmbedder: vi.fn().mockResolvedValue({ valid: true }),
+			}
+			MockedCodeIndexServiceFactory.mockImplementation(() => mockServiceFactoryInstance as any)
+
+			// Act
+			await (manager as any)._recreateServices()
+
+			// Assert
+			expect(mockServiceFactoryInstance.createServices).toHaveBeenCalledTimes(1)
+			const createServicesCall = mockServiceFactoryInstance.createServices.mock.calls[0]
+
+			// Verify parameters: context, cacheManager, ignoreInstance, rooIgnoreController
+			expect(createServicesCall).toHaveLength(4)
+			expect(createServicesCall[0]).toBe(mockContext) // context
+			expect(createServicesCall[1]).toBe(mockCacheManager) // cacheManager
+
+			// Third parameter should be ignore instance with .gitignore patterns
+			const ignoreInstance = createServicesCall[2]
+			expect(ignoreInstance.ignores("node_modules/package.json")).toBe(true)
+			expect(ignoreInstance.ignores("debug.log")).toBe(true)
+			expect(ignoreInstance.ignores(".gitignore")).toBe(true)
+
+			// Fourth parameter should be RooIgnoreController
+			const rooIgnoreController = createServicesCall[3]
+			expect(rooIgnoreController).toBeDefined()
+			expect(rooIgnoreController).toBe((manager as any)._rooIgnoreController)
+		})
+	})
+})
diff --git a/src/services/code-index/__tests__/manager.spec.ts b/src/services/code-index/__tests__/manager.spec.ts
index 8c64c2fdc6..b86afc6a61 100644
--- a/src/services/code-index/__tests__/manager.spec.ts
+++ b/src/services/code-index/__tests__/manager.spec.ts
@@ -12,7 +12,17 @@ vi.mock("vscode", () => ({
 				index: 0,
 			},
 		],
+		createFileSystemWatcher: vi.fn(() => ({
+			onDidCreate: vi.fn(),
+			onDidChange: vi.fn(),
+			onDidDelete: vi.fn(),
+			dispose: vi.fn(),
+		})),
 	},
+	RelativePattern: vi.fn().mockImplementation((base, pattern) => ({
+		base,
+		pattern,
+	})),
 }))
 
 // Mock only the essential dependencies
@@ -178,6 +188,10 @@ describe("CodeIndexManager - handleSettingsChange regression", () => {
 			// Simulate an initialized manager by setting the required properties
 			;(manager as any)._orchestrator = { stopWatcher: vi.fn() }
 			;(manager as any)._searchService = {}
+			;(manager as any)._rooIgnoreController = {
+				dispose: vi.fn(),
+				loadRooIgnore: vi.fn().mockResolvedValue(undefined),
+			}
 
 			// Verify manager is considered initialized
 			expect(manager.isInitialized).toBe(true)
diff --git a/src/services/code-index/manager.ts b/src/services/code-index/manager.ts
index 18e0752c34..f84209c80d 100644
--- a/src/services/code-index/manager.ts
+++ b/src/services/code-index/manager.ts
@@ -12,9 +12,11 @@ import { CacheManager } from "./cache-manager"
 import fs from "fs/promises"
 import ignore from "ignore"
 import path from "path"
+import { findGitignoreFiles } from "../glob/list-files"
 import { t } from "../../i18n"
 import { TelemetryService } from "@roo-code/telemetry"
 import { TelemetryEventName } from "@roo-code/types"
+import { RooIgnoreController } from "../../core/ignore/RooIgnoreController"
 
 export class CodeIndexManager {
 	// --- Singleton Implementation ---
@@ -27,6 +29,7 @@ export class CodeIndexManager {
 	private _orchestrator: CodeIndexOrchestrator | undefined
 	private _searchService: CodeIndexSearchService | undefined
 	private _cacheManager: CacheManager | undefined
+	private _rooIgnoreController: RooIgnoreController | undefined
 
 	public static getInstance(context: vscode.ExtensionContext): CodeIndexManager | undefined {
 		// Use first workspace folder consistently
@@ -70,7 +73,13 @@ export class CodeIndexManager {
 	}
 
 	private assertInitialized() {
-		if (!this._configManager || !this._orchestrator || !this._searchService || !this._cacheManager) {
+		if (
+			!this._configManager ||
+			!this._orchestrator ||
+			!this._searchService ||
+			!this._cacheManager ||
+			!this._rooIgnoreController
+		) {
 			throw new Error("CodeIndexManager not initialized. Call initialize() first.")
 		}
 	}
@@ -100,6 +109,13 @@ export class CodeIndexManager {
 		}
 	}
 
+	/**
+	 * Get the global RooIgnoreController instance
+	 */
+	public get rooIgnoreController(): RooIgnoreController | undefined {
+		return this._rooIgnoreController
+	}
+
 	/**
 	 * Initializes the manager with configuration and dependent services.
 	 * Must be called before using any other methods.
@@ -186,6 +202,9 @@ export class CodeIndexManager {
 		if (this._orchestrator) {
 			this.stopWatcher()
 		}
+		if (this._rooIgnoreController) {
+			this._rooIgnoreController.dispose()
+		}
 		this._stateManager.dispose()
 	}
 
@@ -228,6 +247,7 @@ export class CodeIndexManager {
 		// Clear existing services to ensure clean state
 		this._orchestrator = undefined
 		this._searchService = undefined
+		// Note: Keep _rooIgnoreController to preserve file watchers unless it doesn't exist
 
 		// (Re)Initialize service factory
 		this._serviceFactory = new CodeIndexServiceFactory(
@@ -244,26 +264,41 @@ export class CodeIndexManager {
 			return
 		}
 
-		const ignorePath = path.join(workspacePath, ".gitignore")
+		// Load all .gitignore files from workspace root up to parent directories
 		try {
-			const content = await fs.readFile(ignorePath, "utf8")
-			ignoreInstance.add(content)
+			const gitignoreFiles = await findGitignoreFiles(workspacePath)
+			for (const gitignoreFile of gitignoreFiles) {
+				try {
+					const content = await fs.readFile(gitignoreFile, "utf8")
+					ignoreInstance.add(content)
+				} catch (error) {
+					console.warn(`Failed to read .gitignore file at ${gitignoreFile}:`, error)
+				}
+			}
+			// Always ignore .gitignore files themselves
 			ignoreInstance.add(".gitignore")
 		} catch (error) {
-			// Should never happen: reading file failed even though it exists
-			console.error("Unexpected error loading .gitignore:", error)
+			console.error("Error finding .gitignore files:", error)
 			TelemetryService.instance.captureEvent(TelemetryEventName.CODE_INDEX_ERROR, {
 				error: error instanceof Error ? error.message : String(error),
 				stack: error instanceof Error ? error.stack : undefined,
-				location: "_recreateServices",
+				location: "_recreateServices.gitignore",
 			})
 		}
 
+		// Initialize or reuse RooIgnoreController with file watchers
+		if (!this._rooIgnoreController) {
+			this._rooIgnoreController = new RooIgnoreController(workspacePath)
+		}
+		// Always reload .rooignore patterns to ensure they're up to date
+		await this._rooIgnoreController.loadRooIgnore()
+
 		// (Re)Create shared service instances
 		const { embedder, vectorStore, scanner, fileWatcher } = this._serviceFactory.createServices(
 			this.context,
 			this._cacheManager!,
 			ignoreInstance,
+			this._rooIgnoreController,
 		)
 
 		// Validate embedder configuration before proceeding
diff --git a/src/services/code-index/processors/scanner.ts b/src/services/code-index/processors/scanner.ts
index 538a1252d7..508a9b42a6 100644
--- a/src/services/code-index/processors/scanner.ts
+++ b/src/services/code-index/processors/scanner.ts
@@ -36,6 +36,7 @@ export class DirectoryScanner implements IDirectoryScanner {
 		private readonly codeParser: ICodeParser,
 		private readonly cacheManager: CacheManager,
 		private readonly ignoreInstance: Ignore,
+		private readonly rooIgnoreController?: RooIgnoreController,
 	) {}
 
 	/**
@@ -62,10 +63,15 @@ export class DirectoryScanner implements IDirectoryScanner {
 		// Filter out directories (marked with trailing '/')
 		const filePaths = allPaths.filter((p) => !p.endsWith("/"))
 
-		// Initialize RooIgnoreController if not provided
-		const ignoreController = new RooIgnoreController(directoryPath)
-
-		await ignoreController.initialize()
+		// Use injected RooIgnoreController or create a fallback
+		let ignoreController: RooIgnoreController
+		if (this.rooIgnoreController) {
+			ignoreController = this.rooIgnoreController
+		} else {
+			// Fallback for backward compatibility
+			ignoreController = new RooIgnoreController(directoryPath)
+			await ignoreController.initialize()
+		}
 
 		// Filter paths using .rooignore
 		const allowedPaths = ignoreController.filterPaths(filePaths)
diff --git a/src/services/code-index/service-factory.ts b/src/services/code-index/service-factory.ts
index a741aaf72a..256c9db66b 100644
--- a/src/services/code-index/service-factory.ts
+++ b/src/services/code-index/service-factory.ts
@@ -10,6 +10,7 @@ import { ICodeParser, IEmbedder, IFileWatcher, IVectorStore } from "./interfaces
 import { CodeIndexConfigManager } from "./config-manager"
 import { CacheManager } from "./cache-manager"
 import { Ignore } from "ignore"
+import { RooIgnoreController } from "../../core/ignore/RooIgnoreController"
 import { t } from "../../i18n"
 import { TelemetryService } from "@roo-code/telemetry"
 import { TelemetryEventName } from "@roo-code/types"
@@ -145,8 +146,16 @@ export class CodeIndexServiceFactory {
 		vectorStore: IVectorStore,
 		parser: ICodeParser,
 		ignoreInstance: Ignore,
+		rooIgnoreController?: RooIgnoreController,
 	): DirectoryScanner {
-		return new DirectoryScanner(embedder, vectorStore, parser, this.cacheManager, ignoreInstance)
+		return new DirectoryScanner(
+			embedder,
+			vectorStore,
+			parser,
+			this.cacheManager,
+			ignoreInstance,
+			rooIgnoreController,
+		)
 	}
 
 	/**
@@ -158,8 +167,17 @@ export class CodeIndexServiceFactory {
 		vectorStore: IVectorStore,
 		cacheManager: CacheManager,
 		ignoreInstance: Ignore,
+		rooIgnoreController?: RooIgnoreController,
 	): IFileWatcher {
-		return new FileWatcher(this.workspacePath, context, cacheManager, embedder, vectorStore, ignoreInstance)
+		return new FileWatcher(
+			this.workspacePath,
+			context,
+			cacheManager,
+			embedder,
+			vectorStore,
+			ignoreInstance,
+			rooIgnoreController,
+		)
 	}
 
 	/**
@@ -170,6 +188,7 @@ export class CodeIndexServiceFactory {
 		context: vscode.ExtensionContext,
 		cacheManager: CacheManager,
 		ignoreInstance: Ignore,
+		rooIgnoreController?: RooIgnoreController,
 	): {
 		embedder: IEmbedder
 		vectorStore: IVectorStore
@@ -184,8 +203,15 @@ export class CodeIndexServiceFactory {
 		const embedder = this.createEmbedder()
 		const vectorStore = this.createVectorStore()
 		const parser = codeParser
-		const scanner = this.createDirectoryScanner(embedder, vectorStore, parser, ignoreInstance)
-		const fileWatcher = this.createFileWatcher(context, embedder, vectorStore, cacheManager, ignoreInstance)
+		const scanner = this.createDirectoryScanner(embedder, vectorStore, parser, ignoreInstance, rooIgnoreController)
+		const fileWatcher = this.createFileWatcher(
+			context,
+			embedder,
+			vectorStore,
+			cacheManager,
+			ignoreInstance,
+			rooIgnoreController,
+		)
 
 		return {
 			embedder,
diff --git a/src/services/glob/list-files.ts b/src/services/glob/list-files.ts
index 3164ed1eb0..dee99780d4 100644
--- a/src/services/glob/list-files.ts
+++ b/src/services/glob/list-files.ts
@@ -184,7 +184,7 @@ async function createIgnoreInstance(dirPath: string): Promise<ReturnType<typeof
 /**
  * Find all .gitignore files from the given directory up to the workspace root
  */
-async function findGitignoreFiles(startPath: string): Promise<string[]> {
+export async function findGitignoreFiles(startPath: string): Promise<string[]> {
 	const gitignoreFiles: string[] = []
 	let currentPath = startPath
 
@@ -312,7 +312,6 @@ function isDirectoryExplicitlyIgnored(dirName: string): boolean {
 	return false
 }
 
-
 /**
  * Combine file and directory results and format them properly
  */