diff --git a/examples/pdf-server/main.ts b/examples/pdf-server/main.ts
index bb7b57f42..bc2e5bba7 100644
--- a/examples/pdf-server/main.ts
+++ b/examples/pdf-server/main.ts
@@ -23,6 +23,7 @@ import {
   cliLocalFiles,
   DEFAULT_PDF,
   allowedLocalDirs,
+  cliLocalDirs,
   writeFlags,
 } from "./server.js";
 
@@ -162,6 +163,7 @@ async function main() {
           console.error(`[pdf-server] Registered local file: ${filePath}`);
         } else if (s.isDirectory()) {
           allowedLocalDirs.add(filePath);
+          cliLocalDirs.add(filePath);
           console.error(`[pdf-server] Registered local directory: ${filePath}`);
         }
       } else {
diff --git a/examples/pdf-server/server.test.ts b/examples/pdf-server/server.test.ts
index 0b2a5eb4d..1fea9f773 100644
--- a/examples/pdf-server/server.test.ts
+++ b/examples/pdf-server/server.test.ts
@@ -20,6 +20,7 @@ import {
   startFileWatch,
   stopFileWatch,
   cliLocalFiles,
+  cliLocalDirs,
   isWritablePath,
   writeFlags,
   viewSourcePaths,
@@ -786,6 +787,31 @@ describe("createServer useClientRoots option", () => {
     expect(server.server.oninitialized).toBeFunction();
     server.close();
   });
+
+  it("preserves CLI directories when the client returns no roots", async () => {
+    const cliDir = "/cli/documents";
+    const previousClientDir = "/client/documents";
+    cliLocalDirs.add(cliDir);
+    allowedLocalDirs.add(cliDir);
+    allowedLocalDirs.add(previousClientDir);
+
+    const server = createServer({ useClientRoots: true });
+    try {
+      spyOn(server.server, "getClientCapabilities").mockReturnValue({
+        roots: {},
+      });
+      spyOn(server.server, "listRoots").mockResolvedValue({ roots: [] });
+
+      await server.server.oninitialized?.();
+
+      expect(allowedLocalDirs).toEqual(new Set([cliDir]));
+    } finally {
+      allowedLocalDirs.delete(cliDir);
+      allowedLocalDirs.delete(previousClientDir);
+      cliLocalDirs.delete(cliDir);
+      await server.close();
+    }
+  });
 });
 
 describe("isWritablePath", () => {
diff --git a/examples/pdf-server/server.ts b/examples/pdf-server/server.ts
index e67cd4731..ca2f1816f 100644
--- a/examples/pdf-server/server.ts
+++ b/examples/pdf-server/server.ts
@@ -99,6 +99,9 @@ export const allowedLocalDirs = new Set<string>();
  */
 export const cliLocalFiles = new Set<string>();
 
+/** Directory paths explicitly passed as CLI args. */
+export const cliLocalDirs = new Set<string>();
+
 /**
  * Write-permission flags. Object wrapper (not a bare `let`) so main.ts can
  * mutate via the exported binding without re-import gymnastics — same
@@ -954,6 +957,7 @@ async function refreshRoots(server: Server): Promise<void> {
   try {
     const { roots } = await server.listRoots();
     allowedLocalDirs.clear();
+    for (const dir of cliLocalDirs) allowedLocalDirs.add(dir);
     for (const root of roots) {
       if (isFileUrl(root.uri)) {
         const dir = fileUrlToPath(root.uri);
@@ -1275,8 +1279,8 @@ export function createServer(options: CreateServerOptions = {}): McpServer {
 
   if (useClientRoots) {
     // Fetch roots on initialization and subscribe to changes
-    server.server.oninitialized = () => {
-      refreshRoots(server.server);
+    server.server.oninitialized = async () => {
+      await refreshRoots(server.server);
     };
     server.server.setNotificationHandler(
       "notifications/roots/list_changed",