diff --git a/src/filesystem/__tests__/path-validation.test.ts b/src/filesystem/__tests__/path-validation.test.ts
index 81ad247ee2..230e1dde9c 100644
--- a/src/filesystem/__tests__/path-validation.test.ts
+++ b/src/filesystem/__tests__/path-validation.test.ts
@@ -199,9 +199,9 @@ describe('Path Validation', () => {
       expect(isPathWithinAllowedDirectories('/home/user/café', allowed)).toBe(true);
       expect(isPathWithinAllowedDirectories('/home/user/café/file', allowed)).toBe(true);
 
-      // Different unicode representation won't match (not normalized)
+      // Different unicode representations now match after NFC normalization
       const decomposed = '/home/user/cafe\u0301'; // e + combining accent
-      expect(isPathWithinAllowedDirectories(decomposed, allowed)).toBe(false);
+      expect(isPathWithinAllowedDirectories(decomposed, allowed)).toBe(true);
     });
 
     it('handles paths with spaces correctly', () => {
diff --git a/src/filesystem/index.ts b/src/filesystem/index.ts
index 7b67e63e58..998a35a7ae 100644
--- a/src/filesystem/index.ts
+++ b/src/filesystem/index.ts
@@ -717,7 +717,10 @@ 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.
 server.server.setNotificationHandler(RootsListChangedNotificationSchema, async () => {
   try {
-    // Request the updated roots list from the client
+    // Only update from MCP roots if no CLI directories were set
+    if (allowedDirectories.length > 0) {
+      return;
+    }
     const response = await server.server.listRoots();
     if (response && 'roots' in response) {
       await updateAllowedDirectoriesFromRoots(response.roots);
diff --git a/src/filesystem/path-validation.ts b/src/filesystem/path-validation.ts
index 972e9c49d0..3c2adc8358 100644
--- a/src/filesystem/path-validation.ts
+++ b/src/filesystem/path-validation.ts
@@ -27,7 +27,7 @@ export function isPathWithinAllowedDirectories(absolutePath: string, allowedDire
   // Normalize the input path
   let normalizedPath: string;
   try {
-    normalizedPath = path.resolve(path.normalize(absolutePath));
+    normalizedPath = path.resolve(path.normalize(absolutePath)).normalize("NFC");
   } catch {
     return false;
   }
@@ -51,7 +51,7 @@ export function isPathWithinAllowedDirectories(absolutePath: string, allowedDire
     // Normalize the allowed directory
     let normalizedDir: string;
     try {
-      normalizedDir = path.resolve(path.normalize(dir));
+      normalizedDir = path.resolve(path.normalize(dir)).normalize("NFC");
     } catch {
       return false;
     }