diff --git a/src/core/webview/webviewMessageHandler.ts b/src/core/webview/webviewMessageHandler.ts
index 97ef0ddc3c..b25c3957a2 100644
--- a/src/core/webview/webviewMessageHandler.ts
+++ b/src/core/webview/webviewMessageHandler.ts
@@ -43,7 +43,7 @@ import { getOpenAiModels } from "../../api/providers/openai"
 import { getVsCodeLmModels } from "../../api/providers/vscode-lm"
 import { openMention } from "../mentions"
 import { TelemetrySetting } from "../../shared/TelemetrySetting"
-import { getWorkspacePath } from "../../utils/path"
+import { getWorkspacePath, findWorkspaceWithRoo } from "../../utils/path"
 import { ensureSettingsDirectoryExists } from "../../utils/globalContext"
 import { Mode, defaultModeSlug } from "../../shared/modes"
 import { getModels, flushModels } from "../../api/providers/fetchers/modelCache"
@@ -2477,13 +2477,13 @@ export const webviewMessageHandler = async (
 					const globalConfigDir = path.join(os.homedir(), ".roo")
 					commandsDir = path.join(globalConfigDir, "commands")
 				} else {
-					// Project commands
-					const workspaceRoot = vscode.workspace.workspaceFolders?.[0]?.uri.fsPath
-					if (!workspaceRoot) {
+					// Project commands - find the workspace with .roo directory
+					const workspaceWithRoo = await findWorkspaceWithRoo()
+					if (!workspaceWithRoo) {
 						vscode.window.showErrorMessage(t("common:errors.no_workspace_for_project_command"))
 						break
 					}
-					commandsDir = path.join(workspaceRoot, ".roo", "commands")
+					commandsDir = path.join(workspaceWithRoo.uri.fsPath, ".roo", "commands")
 				}
 
 				// Ensure the commands directory exists
diff --git a/src/utils/__tests__/path.spec.ts b/src/utils/__tests__/path.spec.ts
index a8cf84b68c..f159b84145 100644
--- a/src/utils/__tests__/path.spec.ts
+++ b/src/utils/__tests__/path.spec.ts
@@ -3,9 +3,18 @@
 import os from "os"
 import * as path from "path"
 
-import { arePathsEqual, getReadablePath, getWorkspacePath } from "../path"
+// Use vi.hoisted to ensure mocks are available during module loading
+const { mockWorkspaceFolders, mockGetWorkspaceFolder, mockFileExistsAtPath } = vi.hoisted(() => {
+	const mockWorkspaceFolders = vi.fn()
+	const mockGetWorkspaceFolder = vi.fn()
+	const mockFileExistsAtPath = vi.fn()
+	return { mockWorkspaceFolders, mockGetWorkspaceFolder, mockFileExistsAtPath }
+})
 
-// Mock modules
+// Mock modules before imports
+vi.mock("../fs", () => ({
+	fileExistsAtPath: mockFileExistsAtPath,
+}))
 
 vi.mock("vscode", () => ({
 	window: {
@@ -16,23 +25,37 @@ vi.mock("vscode", () => ({
 		},
 	},
 	workspace: {
-		workspaceFolders: [
+		get workspaceFolders() {
+			return mockWorkspaceFolders()
+		},
+		getWorkspaceFolder: mockGetWorkspaceFolder,
+	},
+}))
+
+import { arePathsEqual, getReadablePath, getWorkspacePath, findWorkspaceWithRoo } from "../path"
+import { fileExistsAtPath } from "../fs"
+
+describe("Path Utilities", () => {
+	const originalPlatform = process.platform
+	// Helper to mock VS Code configuration
+
+	beforeEach(() => {
+		// Reset mocks before each test
+		vi.clearAllMocks()
+		// Set default workspace folders
+		mockWorkspaceFolders.mockReturnValue([
 			{
 				uri: { fsPath: "/test/workspace" },
 				name: "test",
 				index: 0,
 			},
-		],
-		getWorkspaceFolder: vi.fn().mockReturnValue({
+		])
+		mockGetWorkspaceFolder.mockReturnValue({
 			uri: {
 				fsPath: "/test/workspaceFolder",
 			},
-		}),
-	},
-}))
-describe("Path Utilities", () => {
-	const originalPlatform = process.platform
-	// Helper to mock VS Code configuration
+		})
+	})
 
 	afterEach(() => {
 		Object.defineProperty(process, "platform", {
diff --git a/src/utils/path.ts b/src/utils/path.ts
index 48e2ce6673..903cc8d876 100644
--- a/src/utils/path.ts
+++ b/src/utils/path.ts
@@ -1,6 +1,7 @@
 import * as path from "path"
 import os from "os"
 import * as vscode from "vscode"
+import { fileExistsAtPath } from "./fs"
 
 /*
 The Node.js 'path' module resolves and normalizes paths differently depending on the platform:
@@ -130,3 +131,33 @@ export const getWorkspacePathForContext = (contextPath?: string): string => {
 	// Fall back to current behavior
 	return getWorkspacePath()
 }
+
+/**
+ * Finds the workspace folder that contains a .roo directory.
+ * In multi-root workspaces, this ensures we find the correct workspace
+ * rather than just using the first one.
+ *
+ * @returns The workspace folder containing .roo, or undefined if none found
+ */
+export async function findWorkspaceWithRoo(): Promise<vscode.WorkspaceFolder | undefined> {
+	const workspaceFolders = vscode.workspace.workspaceFolders
+	if (!workspaceFolders || workspaceFolders.length === 0) {
+		return undefined
+	}
+
+	// If there's only one workspace folder, return it
+	if (workspaceFolders.length === 1) {
+		return workspaceFolders[0]
+	}
+
+	// Check each workspace folder for a .roo directory
+	for (const folder of workspaceFolders) {
+		const rooPath = path.join(folder.uri.fsPath, ".roo")
+		if (await fileExistsAtPath(rooPath)) {
+			return folder
+		}
+	}
+
+	// If no .roo directory found in any workspace, return the first one as fallback
+	return workspaceFolders[0]
+}