diff --git a/src/agents/workspace.ts b/src/agents/workspace.ts
index bf5f33992a0..953a28ec300 100644
--- a/src/agents/workspace.ts
+++ b/src/agents/workspace.ts
@@ -102,6 +102,11 @@ type WorkspaceOnboardingState = {
   onboardingCompletedAt?: string;
 };
 
+export type WorkspaceOnboardingStateSnapshot = {
+  bootstrapSeededAt?: string;
+  onboardingCompletedAt?: string;
+};
+
 /** Set of recognized bootstrap filenames for runtime validation */
 const VALID_BOOTSTRAP_NAMES: ReadonlySet<string> = new Set([
   DEFAULT_AGENTS_FILENAME,
@@ -184,6 +189,24 @@ async function readWorkspaceOnboardingState(statePath: string): Promise<Workspac
   }
 }
 
+export async function readWorkspaceOnboardingStateForDir(
+  dir: string,
+): Promise<WorkspaceOnboardingStateSnapshot> {
+  const statePath = resolveWorkspaceStatePath(resolveUserPath(dir));
+  const state = await readWorkspaceOnboardingState(statePath);
+  return {
+    bootstrapSeededAt: state.bootstrapSeededAt,
+    onboardingCompletedAt: state.onboardingCompletedAt,
+  };
+}
+
+export async function isWorkspaceOnboardingCompleted(dir: string): Promise<boolean> {
+  const state = await readWorkspaceOnboardingStateForDir(dir);
+  return (
+    typeof state.onboardingCompletedAt === "string" && state.onboardingCompletedAt.trim().length > 0
+  );
+}
+
 async function writeWorkspaceOnboardingState(
   statePath: string,
   state: WorkspaceOnboardingState,
diff --git a/src/gateway/server-methods/agents-mutate.test.ts b/src/gateway/server-methods/agents-mutate.test.ts
index bd5cc5cc3cc..c999f92def8 100644
--- a/src/gateway/server-methods/agents-mutate.test.ts
+++ b/src/gateway/server-methods/agents-mutate.test.ts
@@ -25,6 +25,8 @@ const mocks = vi.hoisted(() => ({
   fsAccess: vi.fn(async () => {}),
   fsMkdir: vi.fn(async () => undefined),
   fsAppendFile: vi.fn(async () => {}),
+  fsReadFile: vi.fn(async () => ""),
+  fsStat: vi.fn(async () => null),
 }));
 
 vi.mock("../../config/config.js", () => ({
@@ -81,6 +83,8 @@ vi.mock("node:fs/promises", async () => {
     access: mocks.fsAccess,
     mkdir: mocks.fsMkdir,
     appendFile: mocks.fsAppendFile,
+    readFile: mocks.fsReadFile,
+    stat: mocks.fsStat,
   };
   return { ...patched, default: patched };
 });
@@ -109,6 +113,21 @@ function makeCall(method: keyof typeof agentsHandlers, params: Record<string, un
   return { respond, promise };
 }
 
+function createEnoentError() {
+  const err = new Error("ENOENT") as NodeJS.ErrnoException;
+  err.code = "ENOENT";
+  return err;
+}
+
+beforeEach(() => {
+  mocks.fsReadFile.mockImplementation(async () => {
+    throw createEnoentError();
+  });
+  mocks.fsStat.mockImplementation(async () => {
+    throw createEnoentError();
+  });
+});
+
 /* ------------------------------------------------------------------ */
 /* Tests                                                              */
 /* ------------------------------------------------------------------ */
@@ -371,3 +390,37 @@ describe("agents.delete", () => {
     );
   });
 });
+
+describe("agents.files.list", () => {
+  beforeEach(() => {
+    vi.clearAllMocks();
+    mocks.loadConfigReturn = {};
+  });
+
+  it("includes BOOTSTRAP.md when onboarding has not completed", async () => {
+    const { respond, promise } = makeCall("agents.files.list", { agentId: "main" });
+    await promise;
+
+    const [, result] = respond.mock.calls[0] ?? [];
+    const files = (result as { files: Array<{ name: string }> }).files;
+    expect(files.some((file) => file.name === "BOOTSTRAP.md")).toBe(true);
+  });
+
+  it("hides BOOTSTRAP.md when workspace onboarding is complete", async () => {
+    mocks.fsReadFile.mockImplementation(async (filePath: string | URL | number) => {
+      if (String(filePath).endsWith("workspace-state.json")) {
+        return JSON.stringify({
+          onboardingCompletedAt: "2026-02-15T14:00:00.000Z",
+        });
+      }
+      throw createEnoentError();
+    });
+
+    const { respond, promise } = makeCall("agents.files.list", { agentId: "main" });
+    await promise;
+
+    const [, result] = respond.mock.calls[0] ?? [];
+    const files = (result as { files: Array<{ name: string }> }).files;
+    expect(files.some((file) => file.name === "BOOTSTRAP.md")).toBe(false);
+  });
+});
diff --git a/src/gateway/server-methods/agents.ts b/src/gateway/server-methods/agents.ts
index eb4262e43fd..f1a1dc986af 100644
--- a/src/gateway/server-methods/agents.ts
+++ b/src/gateway/server-methods/agents.ts
@@ -17,6 +17,7 @@ import {
   DEFAULT_TOOLS_FILENAME,
   DEFAULT_USER_FILENAME,
   ensureAgentWorkspace,
+  isWorkspaceOnboardingCompleted,
 } from "../../agents/workspace.js";
 import { movePathToTrash } from "../../browser/trash.js";
 import {
@@ -52,6 +53,9 @@ const BOOTSTRAP_FILE_NAMES = [
   DEFAULT_HEARTBEAT_FILENAME,
   DEFAULT_BOOTSTRAP_FILENAME,
 ] as const;
+const BOOTSTRAP_FILE_NAMES_WITHOUT_ONBOARDING = BOOTSTRAP_FILE_NAMES.filter(
+  (name) => name !== DEFAULT_BOOTSTRAP_FILENAME,
+);
 
 const MEMORY_FILE_NAMES = [DEFAULT_MEMORY_FILENAME, DEFAULT_MEMORY_ALT_FILENAME] as const;
 
@@ -108,7 +112,7 @@ async function statFile(filePath: string): Promise<FileMeta | null> {
   }
 }
 
-async function listAgentFiles(workspaceDir: string) {
+async function listAgentFiles(workspaceDir: string, options?: { hideBootstrap?: boolean }) {
   const files: Array<{
     name: string;
     path: string;
@@ -117,7 +121,10 @@ async function listAgentFiles(workspaceDir: string) {
     updatedAtMs?: number;
   }> = [];
 
-  for (const name of BOOTSTRAP_FILE_NAMES) {
+  const bootstrapFileNames = options?.hideBootstrap
+    ? BOOTSTRAP_FILE_NAMES_WITHOUT_ONBOARDING
+    : BOOTSTRAP_FILE_NAMES;
+  for (const name of bootstrapFileNames) {
     const filePath = path.join(workspaceDir, name);
     const meta = await statFile(filePath);
     if (meta) {
@@ -417,7 +424,13 @@ export const agentsHandlers: GatewayRequestHandlers = {
       return;
     }
     const workspaceDir = resolveAgentWorkspaceDir(cfg, agentId);
-    const files = await listAgentFiles(workspaceDir);
+    let hideBootstrap = false;
+    try {
+      hideBootstrap = await isWorkspaceOnboardingCompleted(workspaceDir);
+    } catch {
+      // Fall back to showing BOOTSTRAP if workspace state cannot be read.
+    }
+    const files = await listAgentFiles(workspaceDir, { hideBootstrap });
     respond(true, { agentId, workspace: workspaceDir, files }, undefined);
   },
   "agents.files.get": async ({ params, respond }) => {