diff --git a/src/filesystem/__tests__/roots-merge.test.ts b/src/filesystem/__tests__/roots-merge.test.ts
new file mode 100644
index 0000000000..108b0e1585
--- /dev/null
+++ b/src/filesystem/__tests__/roots-merge.test.ts
@@ -0,0 +1,73 @@
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { mkdtempSync, rmSync, realpathSync } from 'fs';
+import { tmpdir } from 'os';
+import { join } from 'path';
+
+describe('updateAllowedDirectoriesFromRoots merge behaviour', () => {
+  let cliDir: string;
+  let mcpDir1: string;
+  let mcpDir2: string;
+
+  beforeEach(() => {
+    cliDir = realpathSync(mkdtempSync(join(tmpdir(), 'mcp-cli-')));
+    mcpDir1 = realpathSync(mkdtempSync(join(tmpdir(), 'mcp-roots1-')));
+    mcpDir2 = realpathSync(mkdtempSync(join(tmpdir(), 'mcp-roots2-')));
+  });
+
+  afterEach(() => {
+    rmSync(cliDir, { recursive: true, force: true });
+    rmSync(mcpDir1, { recursive: true, force: true });
+    rmSync(mcpDir2, { recursive: true, force: true });
+  });
+
+  it('should preserve CLI dirs after init with roots', () => {
+    // Simulates the snapshot: cliAllowedDirectories = [cliDir]
+    const cliAllowedDirectories = [cliDir];
+    const validatedRootDirs = [mcpDir1];
+
+    const merged = new Set([...cliAllowedDirectories, ...validatedRootDirs]);
+    const allowedDirectories = [...merged];
+
+    expect(allowedDirectories).toContain(cliDir);
+    expect(allowedDirectories).toContain(mcpDir1);
+  });
+
+  it('should replace MCP roots on roots/list_changed without accumulating', () => {
+    // Simulates: CLI dir + first MCP root
+    const cliAllowedDirectories = [cliDir];
+    const firstMcpRoots = [mcpDir1];
+
+    let merged = new Set([...cliAllowedDirectories, ...firstMcpRoots]);
+    let allowedDirectories = [...merged];
+
+    expect(allowedDirectories).toContain(cliDir);
+    expect(allowedDirectories).toContain(mcpDir1);
+    expect(allowedDirectories).toHaveLength(2);
+
+    // Simulates: roots/list_changed with new root (mcpDir2 replaces mcpDir1)
+    const secondMcpRoots = [mcpDir2];
+    merged = new Set([...cliAllowedDirectories, ...secondMcpRoots]);
+    allowedDirectories = [...merged];
+
+    expect(allowedDirectories).toContain(cliDir);
+    expect(allowedDirectories).toContain(mcpDir2);
+    expect(allowedDirectories).not.toContain(mcpDir1);
+    expect(allowedDirectories).toHaveLength(2);
+  });
+
+  it('should not accumulate stale roots across multiple updates', () => {
+    const cliAllowedDirectories = [cliDir];
+    let allowedDirectories: string[] = [];
+
+    for (let i = 0; i < 5; i++) {
+      const tmpDir = realpathSync(mkdtempSync(join(tmpdir(), `mcp-root-${i}-`)));
+      const merged = new Set([...cliAllowedDirectories, tmpDir]);
+      allowedDirectories = [...merged];
+      rmSync(tmpDir, { recursive: true, force: true });
+    }
+
+    // After each iteration, only CLI dir + latest root should be present
+    expect(allowedDirectories).toHaveLength(2);
+    expect(allowedDirectories).toContain(cliDir);
+  });
+});
diff --git a/src/filesystem/index.ts b/src/filesystem/index.ts
index 7b67e63e58..cd55b8974e 100644
--- a/src/filesystem/index.ts
+++ b/src/filesystem/index.ts
@@ -89,6 +89,10 @@ if (accessibleDirectories.length === 0 && allowedDirectories.length > 0) {
 
 allowedDirectories = accessibleDirectories;
 
+// Save CLI-provided directories separately so dynamic MCP roots updates
+// can replace the previous MCP roots without losing CLI dirs or accumulating stale ones.
+const cliAllowedDirectories = [...allowedDirectories];
+
 // Initialize the global allowedDirectories in lib.ts
 setAllowedDirectories(allowedDirectories);
 
@@ -706,7 +710,10 @@ server.registerTool(
 async function updateAllowedDirectoriesFromRoots(requestedRoots: Root[]) {
   const validatedRootDirs = await getValidRootDirectories(requestedRoots);
   if (validatedRootDirs.length > 0) {
-    allowedDirectories = [...validatedRootDirs];
+    // Merge CLI-provided directories with current MCP roots,
+    // replacing any previous MCP roots on each update.
+    const merged = new Set([...cliAllowedDirectories, ...validatedRootDirs]);
+    allowedDirectories = [...merged];
     setAllowedDirectories(allowedDirectories); // Update the global state in lib.ts
     console.error(`Updated allowed directories from MCP roots: ${validatedRootDirs.length} valid directories`);
   } else {
@@ -714,7 +721,7 @@ async function updateAllowedDirectoriesFromRoots(requestedRoots: Root[]) {
   }
 }
 
-// Handles dynamic roots updates during runtime, when client sends "roots/list_changed" notification, server fetches the updated roots and replaces all allowed directories with the new roots.
+// Handles dynamic roots updates during runtime, when client sends "roots/list_changed" notification, server fetches the updated roots and merges them with CLI-provided directories (replacing any previous MCP roots).
 server.server.setNotificationHandler(RootsListChangedNotificationSchema, async () => {
   try {
     // Request the updated roots list from the client