diff --git a/src/filesystem/__tests__/roots-utils.test.ts b/src/filesystem/__tests__/roots-utils.test.ts
index 1a39483953..27d500311d 100644
--- a/src/filesystem/__tests__/roots-utils.test.ts
+++ b/src/filesystem/__tests__/roots-utils.test.ts
@@ -1,10 +1,22 @@
 import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import { getValidRootDirectories } from '../roots-utils.js';
+import { formatEffectiveAllowedDirectories, getValidRootDirectories } from '../roots-utils.js';
 import { mkdtempSync, rmSync, mkdirSync, writeFileSync, realpathSync } from 'fs';
 import { tmpdir } from 'os';
 import { join } from 'path';
 import type { Root } from '@modelcontextprotocol/sdk/types.js';
 
+describe('formatEffectiveAllowedDirectories', () => {
+  it('includes the source and effective directories', () => {
+    expect(formatEffectiveAllowedDirectories(['/workspace', '/data'], 'client-provided MCP Roots'))
+      .toBe('Effective allowed directories (source: client-provided MCP Roots):\n  /workspace\n  /data');
+  });
+
+  it('marks an empty effective directory set', () => {
+    expect(formatEffectiveAllowedDirectories([], 'none'))
+      .toBe('Effective allowed directories (source: none):\n  (none)');
+  });
+});
+
 describe('getValidRootDirectories', () => {
   let testDir1: string;
   let testDir2: string;
@@ -81,4 +93,4 @@ describe('getValidRootDirectories', () => {
       expect(result).toHaveLength(1);
     });
   });
-});
\ No newline at end of file
+});
diff --git a/src/filesystem/index.ts b/src/filesystem/index.ts
index 51ac523a66..976c990d03 100644
--- a/src/filesystem/index.ts
+++ b/src/filesystem/index.ts
@@ -13,7 +13,7 @@ import { pathToFileURL } from "url";
 import { z } from "zod";
 import { minimatch } from "minimatch";
 import { normalizePath, expandHome } from './path-utils.js';
-import { getValidRootDirectories } from './roots-utils.js';
+import { formatEffectiveAllowedDirectories, getValidRootDirectories } from './roots-utils.js';
 import {
   // Function imports
   formatSize,
@@ -90,6 +90,12 @@ if (accessibleDirectories.length === 0 && allowedDirectories.length > 0) {
 
 allowedDirectories = accessibleDirectories;
 
+let allowedDirectoriesSource = allowedDirectories.length > 0 ? "server arguments" : "none";
+
+function logEffectiveAllowedDirectories() {
+  console.error(formatEffectiveAllowedDirectories(allowedDirectories, allowedDirectoriesSource));
+}
+
 // Initialize the global allowedDirectories in lib.ts
 setAllowedDirectories(allowedDirectories);
 
@@ -726,10 +732,13 @@ async function updateAllowedDirectoriesFromRoots(requestedRoots: Root[]) {
   const validatedRootDirs = await getValidRootDirectories(requestedRoots);
   if (validatedRootDirs.length > 0) {
     allowedDirectories = [...validatedRootDirs];
+    allowedDirectoriesSource = "client-provided MCP Roots";
     setAllowedDirectories(allowedDirectories); // Update the global state in lib.ts
     console.error(`Updated allowed directories from MCP roots: ${validatedRootDirs.length} valid directories`);
+    logEffectiveAllowedDirectories();
   } else {
-    console.error("No valid root directories provided by client");
+    console.error("No valid root directories provided by client; retaining current allowed directories");
+    logEffectiveAllowedDirectories();
   }
 }
 
@@ -757,14 +766,18 @@ server.server.oninitialized = async () => {
         await updateAllowedDirectoriesFromRoots(response.roots);
       } else {
         console.error("Client returned no roots set, keeping current settings");
+        logEffectiveAllowedDirectories();
       }
     } catch (error) {
       console.error("Failed to request initial roots from client:", error instanceof Error ? error.message : String(error));
+      logEffectiveAllowedDirectories();
     }
   } else {
     if (allowedDirectories.length > 0) {
-      console.error("Client does not support MCP Roots, using allowed directories set from server args:", allowedDirectories);
+      console.error("Client does not support MCP Roots");
+      logEffectiveAllowedDirectories();
     }else{
+      logEffectiveAllowedDirectories();
       throw new Error(`Server cannot operate: No allowed directories available. Server was started without command-line directories and client either does not support MCP roots protocol or provided empty roots. Please either: 1) Start server with directory arguments, or 2) Use a client that supports MCP roots protocol and provides valid root directories.`);
     }
   }
diff --git a/src/filesystem/roots-utils.ts b/src/filesystem/roots-utils.ts
index 5e26bb246b..af214944dd 100644
--- a/src/filesystem/roots-utils.ts
+++ b/src/filesystem/roots-utils.ts
@@ -5,6 +5,14 @@ import { normalizePath } from './path-utils.js';
 import type { Root } from '@modelcontextprotocol/sdk/types.js';
 import { fileURLToPath } from "url";
 
+export function formatEffectiveAllowedDirectories(
+  directories: readonly string[],
+  source: string
+): string {
+  const entries = directories.length > 0 ? directories.map(directory => `  ${directory}`) : ["  (none)"];
+  return [`Effective allowed directories (source: ${source}):`, ...entries].join("\n");
+}
+
 /**
  * Converts a root URI to a normalized directory path with basic security validation.
  * @param rootUri - File URI (file://...) or plain directory path
@@ -74,4 +82,4 @@ export async function getValidRootDirectories(
   }
   
   return validatedDirectories;
-}
\ No newline at end of file
+}