diff --git a/packages/types/src/codebase-index.ts b/packages/types/src/codebase-index.ts
index be7778f538..0d72f76c83 100644
--- a/packages/types/src/codebase-index.ts
+++ b/packages/types/src/codebase-index.ts
@@ -36,6 +36,15 @@ export const codebaseIndexConfigSchema = z.object({
 	// OpenAI Compatible specific fields
 	codebaseIndexOpenAiCompatibleBaseUrl: z.string().optional(),
 	codebaseIndexOpenAiCompatibleModelDimension: z.number().optional(),
+	// Per-workspace settings
+	codebaseIndexWorkspaceSettings: z
+		.record(
+			z.string(),
+			z.object({
+				enabled: z.boolean(),
+			}),
+		)
+		.optional(),
 })
 
 export type CodebaseIndexConfig = z.infer<typeof codebaseIndexConfigSchema>
diff --git a/src/core/webview/webviewMessageHandler.ts b/src/core/webview/webviewMessageHandler.ts
index accb66f6e9..bd0a923a6f 100644
--- a/src/core/webview/webviewMessageHandler.ts
+++ b/src/core/webview/webviewMessageHandler.ts
@@ -25,6 +25,7 @@ import { changeLanguage, t } from "../../i18n"
 import { Package } from "../../shared/package"
 import { type RouterName, type ModelRecord, toRouterName } from "../../shared/api"
 import { MessageEnhancer } from "./messageEnhancer"
+import { CodeIndexManager } from "../../services/code-index/manager"
 
 import {
 	type WebviewMessage,
@@ -2569,6 +2570,29 @@ export const webviewMessageHandler = async (
 			})
 			break
 		}
+		case "setWorkspaceCodebaseIndexEnabled": {
+			const { workspacePath, enabled } = message
+			try {
+				const manager = CodeIndexManager.getInstance(provider.context, workspacePath)
+				if (manager && enabled !== undefined) {
+					await manager.setWorkspaceEnabled(enabled)
+
+					// Send updated status back to webview
+					const status = manager.getCurrentStatus()
+					provider.postMessageToWebview({
+						type: "indexingStatusUpdate",
+						values: {
+							...status,
+							workspaceEnabled: manager.getWorkspaceEnabled(),
+							globalEnabled: manager.getGlobalEnabled(),
+						},
+					})
+				}
+			} catch (error) {
+				console.error("Failed to set workspace codebase index enabled state:", error)
+			}
+			break
+		}
 		case "startIndexing": {
 			try {
 				const manager = provider.getCurrentWorkspaceCodeIndexManager()
diff --git a/src/services/code-index/config-manager.ts b/src/services/code-index/config-manager.ts
index 2c0e8bb5c9..bfcc2733f1 100644
--- a/src/services/code-index/config-manager.ts
+++ b/src/services/code-index/config-manager.ts
@@ -25,7 +25,15 @@ export class CodeIndexConfigManager {
 	private searchMinScore?: number
 	private searchMaxResults?: number
 
-	constructor(private readonly contextProxy: ContextProxy) {
+	// Per-workspace settings
+	private workspaceSettings: Record<string, { enabled: boolean }> = {}
+	private currentWorkspacePath: string | undefined
+
+	constructor(
+		private readonly contextProxy: ContextProxy,
+		workspacePath?: string,
+	) {
+		this.currentWorkspacePath = workspacePath
 		// Initialize with current configuration to avoid false restart triggers
 		this._loadAndSetConfiguration()
 	}
@@ -61,6 +69,7 @@ export class CodeIndexConfigManager {
 			codebaseIndexEmbedderModelId,
 			codebaseIndexSearchMinScore,
 			codebaseIndexSearchMaxResults,
+			codebaseIndexWorkspaceSettings,
 		} = codebaseIndexConfig
 
 		const openAiKey = this.contextProxy?.getSecret("codeIndexOpenAiKey") ?? ""
@@ -72,8 +81,20 @@ export class CodeIndexConfigManager {
 		const mistralApiKey = this.contextProxy?.getSecret("codebaseIndexMistralApiKey") ?? ""
 		const vercelAiGatewayApiKey = this.contextProxy?.getSecret("codebaseIndexVercelAiGatewayApiKey") ?? ""
 
+		// Load workspace settings
+		this.workspaceSettings = codebaseIndexWorkspaceSettings ?? {}
+
+		// Determine effective enabled state based on workspace override
+		const globalEnabled = codebaseIndexEnabled ?? true
+		let effectiveEnabled = globalEnabled
+
+		if (this.currentWorkspacePath && this.workspaceSettings[this.currentWorkspacePath]) {
+			// Workspace setting takes precedence over global setting
+			effectiveEnabled = this.workspaceSettings[this.currentWorkspacePath].enabled
+		}
+
 		// Update instance variables with configuration
-		this.codebaseIndexEnabled = codebaseIndexEnabled ?? true
+		this.codebaseIndexEnabled = effectiveEnabled
 		this.qdrantUrl = codebaseIndexQdrantUrl
 		this.qdrantApiKey = qdrantApiKey ?? ""
 		this.searchMinScore = codebaseIndexSearchMinScore
@@ -409,6 +430,47 @@ export class CodeIndexConfigManager {
 		return this.codebaseIndexEnabled
 	}
 
+	/**
+	 * Updates the enabled state for a specific workspace
+	 */
+	public async setWorkspaceEnabled(workspacePath: string, enabled: boolean): Promise<void> {
+		if (!this.contextProxy) {
+			return
+		}
+
+		// Get current config
+		const currentConfig = this.contextProxy.getGlobalState("codebaseIndexConfig") ?? {}
+
+		// Update workspace settings
+		const workspaceSettings = currentConfig.codebaseIndexWorkspaceSettings ?? {}
+		workspaceSettings[workspacePath] = { enabled }
+
+		// Save updated config
+		await this.contextProxy.updateGlobalState("codebaseIndexConfig", {
+			...currentConfig,
+			codebaseIndexWorkspaceSettings: workspaceSettings,
+		})
+
+		// Reload configuration to apply changes
+		await this.loadConfiguration()
+	}
+
+	/**
+	 * Gets the enabled state for a specific workspace
+	 */
+	public getWorkspaceEnabled(workspacePath: string): boolean | undefined {
+		const config = this.contextProxy?.getGlobalState("codebaseIndexConfig") ?? {}
+		return config.codebaseIndexWorkspaceSettings?.[workspacePath]?.enabled
+	}
+
+	/**
+	 * Gets the global enabled state (without workspace override)
+	 */
+	public getGlobalEnabled(): boolean {
+		const config = this.contextProxy?.getGlobalState("codebaseIndexConfig") ?? {}
+		return config.codebaseIndexEnabled ?? true
+	}
+
 	/**
 	 * Gets whether the code indexing feature is properly configured
 	 */
diff --git a/src/services/code-index/manager.ts b/src/services/code-index/manager.ts
index dd79a3f161..ccdca0df0c 100644
--- a/src/services/code-index/manager.ts
+++ b/src/services/code-index/manager.ts
@@ -118,7 +118,7 @@ export class CodeIndexManager {
 	public async initialize(contextProxy: ContextProxy): Promise<{ requiresRestart: boolean }> {
 		// 1. ConfigManager Initialization and Configuration Loading
 		if (!this._configManager) {
-			this._configManager = new CodeIndexConfigManager(contextProxy)
+			this._configManager = new CodeIndexConfigManager(contextProxy, this.workspacePath)
 		}
 		// Load configuration once to get current state and restart requirements
 		const { requiresRestart } = await this._configManager.loadConfiguration()
@@ -419,4 +419,40 @@ export class CodeIndexManager {
 			}
 		}
 	}
+
+	/**
+	 * Sets the enabled state for the current workspace
+	 */
+	public async setWorkspaceEnabled(enabled: boolean): Promise<void> {
+		if (!this._configManager || !this.workspacePath) {
+			return
+		}
+
+		await this._configManager.setWorkspaceEnabled(this.workspacePath, enabled)
+
+		// Reload configuration to apply changes
+		await this.handleSettingsChange()
+	}
+
+	/**
+	 * Gets the enabled state for the current workspace
+	 */
+	public getWorkspaceEnabled(): boolean | undefined {
+		if (!this._configManager || !this.workspacePath) {
+			return undefined
+		}
+
+		return this._configManager.getWorkspaceEnabled(this.workspacePath)
+	}
+
+	/**
+	 * Gets the global enabled state (without workspace override)
+	 */
+	public getGlobalEnabled(): boolean {
+		if (!this._configManager) {
+			return true
+		}
+
+		return this._configManager.getGlobalEnabled()
+	}
 }
diff --git a/src/shared/WebviewMessage.ts b/src/shared/WebviewMessage.ts
index 93d0b9bc45..825f4ac1db 100644
--- a/src/shared/WebviewMessage.ts
+++ b/src/shared/WebviewMessage.ts
@@ -186,6 +186,7 @@ export interface WebviewMessage {
 		| "requestIndexingStatus"
 		| "startIndexing"
 		| "clearIndexData"
+		| "setWorkspaceCodebaseIndexEnabled"
 		| "indexingStatusUpdate"
 		| "indexCleared"
 		| "focusPanelRequest"
@@ -272,6 +273,8 @@ export interface WebviewMessage {
 	checkOnly?: boolean // For deleteCustomMode check
 	upsellId?: string // For dismissUpsell
 	list?: string[] // For dismissedUpsells response
+	workspacePath?: string // For setWorkspaceCodebaseIndexEnabled
+	enabled?: boolean // For setWorkspaceCodebaseIndexEnabled
 	codeIndexSettings?: {
 		// Global state settings
 		codebaseIndexEnabled: boolean