diff --git a/gitnexus/src/mcp/resources.ts b/gitnexus/src/mcp/resources.ts
index 48cd89b57..839139a81 100644
--- a/gitnexus/src/mcp/resources.ts
+++ b/gitnexus/src/mcp/resources.ts
@@ -7,6 +7,7 @@
 
 import type { LocalBackend } from './local/local-backend.js';
 import { checkStaleness } from './staleness.js';
+import { loadMeta } from '../storage/repo-manager.js';
 
 export interface ResourceDefinition {
   uri: string;
@@ -311,9 +312,16 @@ async function getContextResource(backend: LocalBackend, repoName?: string): Pro
     return 'error: No codebase loaded. Run: gitnexus analyze';
   }
 
-  // Check staleness
+  // Read fresh metadata from disk on every context resource read to avoid showing
+  // a stale staleness banner or outdated stats after an out-of-process
+  // `analyze --index-only` refresh. The RepoHandle is cached in-memory and only
+  // refreshes on registry misses, so its lastCommit/stats can lag behind the
+  // on-disk state (#2438). Mirrors the ensureInitialized hot-swap pattern.
+  const freshMeta = await loadMeta(repo.storagePath).catch(() => null);
+
+  // Check staleness using the current on-disk lastCommit (not the cached handle)
   const repoPath = repo.repoPath;
-  const lastCommit = repo.lastCommit || 'HEAD';
+  const lastCommit = freshMeta?.lastCommit ?? repo.lastCommit ?? 'HEAD';
   const staleness = repoPath
     ? checkStaleness(repoPath, lastCommit)
     : { isStale: false, commitsBehind: 0 };
@@ -325,11 +333,13 @@ async function getContextResource(backend: LocalBackend, repoName?: string): Pro
     lines.push(`staleness: "${staleness.hint}"`);
   }
 
+  // Use fresh stats from disk meta when available; fall back to cached context
+  const freshStats = freshMeta?.stats;
   lines.push('');
   lines.push('stats:');
-  lines.push(`  files: ${context.stats.fileCount}`);
-  lines.push(`  symbols: ${context.stats.functionCount}`);
-  lines.push(`  processes: ${context.stats.processCount}`);
+  lines.push(`  files: ${freshStats?.files ?? context.stats.fileCount}`);
+  lines.push(`  symbols: ${freshStats?.nodes ?? context.stats.functionCount}`);
+  lines.push(`  processes: ${freshStats?.processes ?? context.stats.processCount}`);
   lines.push('');
   lines.push('tools_available:');
   lines.push('  - query: Process-grouped code intelligence (execution flows related to a concept)');
diff --git a/gitnexus/test/integration/context-resource-staleness.test.ts b/gitnexus/test/integration/context-resource-staleness.test.ts
new file mode 100644
index 000000000..537a4ae90
--- /dev/null
+++ b/gitnexus/test/integration/context-resource-staleness.test.ts
@@ -0,0 +1,207 @@
+/**
+ * Integration Tests: Context Resource Staleness Fix (#2438)
+ *
+ * End-to-end flow with real git and real registry/meta I/O.
+ */
+import { execFileSync } from 'child_process';
+import { writeFileSync } from 'fs';
+import path from 'path';
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { createTempDir } from '../helpers/test-db.js';
+import type { RepoMeta } from '../../src/storage/repo-manager.js';
+import { getStoragePaths, registerRepo, saveMeta } from '../../src/storage/repo-manager.js';
+
+import { LocalBackend } from '../../src/mcp/local/local-backend.js';
+import { readResource } from '../../src/mcp/resources.js';
+
+// ─── Helpers ─────────────────────────────────────────────────────────────────
+
+function runGit(repoPath: string, ...args: string[]): string {
+  try {
+    return execFileSync('git', args, { cwd: repoPath, encoding: 'utf-8' }).trim();
+  } catch (error) {
+    const message = error instanceof Error ? error.message : String(error);
+    throw new Error(`git ${args.join(' ')} failed in ${repoPath}: ${message}`);
+  }
+}
+
+/**
+ * Persist index metadata and register the repo in the global registry.
+ * `saveMeta` runs before `registerRepo` so registry validation can immediately
+ * see a readable metadata file for this entry.
+ * @param repoPath Absolute path to the git repository under test.
+ * @param storagePath Absolute path to the repo metadata directory.
+ * @param meta Metadata snapshot to write to gitnexus.json and registry.
+ * @param repoName Registry alias used by LocalBackend for this repo.
+ */
+async function seedIndexedRepo(
+  repoPath: string,
+  storagePath: string,
+  meta: RepoMeta,
+  repoName: string = 'test-repo',
+): Promise<void> {
+  await saveMeta(storagePath, meta);
+  await registerRepo(repoPath, meta, { name: repoName });
+}
+
+// ─── Tests ───────────────────────────────────────────────────────────────────
+
+describe('context resource freshness — out-of-process analyze (#2438)', () => {
+  let tmpDir: Awaited<ReturnType<typeof createTempDir>>;
+  let repoPath: string;
+  let storagePath: string;
+  let savedHome: string | undefined;
+
+  beforeEach(async () => {
+    tmpDir = await createTempDir('gnx-ctx-staleness-');
+    repoPath = tmpDir.dbPath;
+
+    // Isolate the global registry from the developer's real ~/.gitnexus
+    savedHome = process.env.GITNEXUS_HOME;
+    process.env.GITNEXUS_HOME = path.join(repoPath, '.gitnexus-home');
+    storagePath = getStoragePaths(repoPath).storagePath;
+
+    runGit(repoPath, 'init');
+    runGit(repoPath, 'config', 'user.name', 'GitNexus Test');
+    runGit(repoPath, 'config', 'user.email', 'gitnexus@example.com');
+  });
+
+  afterEach(async () => {
+    if (savedHome === undefined) delete process.env.GITNEXUS_HOME;
+    else process.env.GITNEXUS_HOME = savedHome;
+    await tmpDir.cleanup();
+  });
+
+  it('clears the staleness banner after out-of-process analyze updates gitnexus.json', async () => {
+    // ── STEP 1: Repository HEAD advances from C1 to C2 ───────────────────────
+    writeFileSync(path.join(repoPath, 'a.ts'), 'export const a = 1;\n');
+    runGit(repoPath, 'add', 'a.ts');
+    runGit(repoPath, 'commit', '-m', 'c1');
+    const c1 = runGit(repoPath, 'rev-parse', 'HEAD');
+    writeFileSync(path.join(repoPath, 'b.ts'), 'export const b = 2;\n');
+    runGit(repoPath, 'add', 'b.ts');
+    runGit(repoPath, 'commit', '-m', 'c2');
+    const c2 = runGit(repoPath, 'rev-parse', 'HEAD');
+
+    const oldStats = { files: 100, nodes: 500, processes: 10 };
+    const freshStats = { files: 120, nodes: 600, processes: 12 };
+
+    await seedIndexedRepo(repoPath, storagePath, {
+      repoPath,
+      lastCommit: c1,
+      indexedAt: '2024-01-01T00:00:00Z',
+      stats: oldStats,
+    });
+
+    const backend = new LocalBackend();
+    await backend.init();
+
+    // C1 is stale against current HEAD (C2)
+    const resultBefore = await readResource(`gitnexus://repo/test-repo/context`, backend);
+    expect(resultBefore).toContain('staleness:');
+    expect(resultBefore).toContain('1 commit behind');
+    // Stats reflect the old (C1-era) values from gitnexus.json
+    expect(resultBefore).toContain('files: 100');
+    expect(resultBefore).toContain('symbols: 500');
+
+    // ── STEP 3: Out-of-process analyze runs, updates gitnexus.json to C2 ───
+    // The MCP server (LocalBackend) is NOT restarted — this is the bug scenario.
+    await saveMeta(storagePath, {
+      repoPath,
+      lastCommit: c2,
+      indexedAt: new Date().toISOString(),
+      stats: freshStats,
+    });
+
+    // ── STEP 4: Re-read context resource WITHOUT restarting the MCP server ──
+    const resultAfter = await readResource(`gitnexus://repo/test-repo/context`, backend);
+
+    // Staleness banner MUST be gone — the fresh gitnexus.json has lastCommit = C2
+    expect(resultAfter).not.toContain('staleness:');
+    // Stats MUST be fresh — taken from the updated gitnexus.json
+    expect(resultAfter).toContain('files: 120');
+    expect(resultAfter).toContain('symbols: 600');
+    expect(resultAfter).toContain('processes: 12');
+  });
+
+  it('shows stale banner before analyze and clears it after — full reproduce sequence', async () => {
+    writeFileSync(path.join(repoPath, 'a.ts'), 'export const a = 1;\n');
+    runGit(repoPath, 'add', 'a.ts');
+    runGit(repoPath, 'commit', '-m', 'c1');
+    writeFileSync(path.join(repoPath, 'b.ts'), 'export const b = 2;\n');
+    runGit(repoPath, 'add', 'b.ts');
+    runGit(repoPath, 'commit', '-m', 'c2');
+    const c2 = runGit(repoPath, 'rev-parse', 'HEAD');
+
+    const stats = { files: 50, nodes: 200, processes: 5 };
+    await seedIndexedRepo(repoPath, storagePath, {
+      repoPath,
+      lastCommit: c2,
+      indexedAt: '2024-01-01T00:00:00Z',
+      stats,
+    });
+
+    const backend = new LocalBackend();
+    await backend.init();
+
+    // Pre-analyze: registry/meta are seeded at current HEAD (C2), so not stale
+    const r1 = await readResource(`gitnexus://repo/test-repo/context`, backend);
+    expect(r1).not.toContain('staleness:');
+
+    // New commit arrives; indexed commit (C2) is stale
+    writeFileSync(path.join(repoPath, 'c.ts'), 'export const c = 3;\n');
+    runGit(repoPath, 'add', 'c.ts');
+    runGit(repoPath, 'commit', '-m', 'c3');
+    const c3 = runGit(repoPath, 'rev-parse', 'HEAD');
+    const r2 = await readResource(`gitnexus://repo/test-repo/context`, backend);
+    expect(r2).toContain('staleness:');
+    expect(r2).toContain('1 commit behind');
+
+    // Out-of-process analyze --index-only completes; gitnexus.json updated to C3
+    const freshStats = { files: 60, nodes: 250, processes: 7 };
+    await saveMeta(storagePath, {
+      repoPath,
+      lastCommit: c3,
+      indexedAt: new Date().toISOString(),
+      stats: freshStats,
+    });
+
+    // Third read — MCP server still running, but context must reflect fresh state
+    const r3 = await readResource(`gitnexus://repo/test-repo/context`, backend);
+    expect(r3).not.toContain('staleness:'); // banner cleared
+    expect(r3).toContain('files: 60'); // fresh stats
+    expect(r3).toContain('symbols: 250');
+    expect(r3).toContain('processes: 7');
+  });
+
+  it('stat fields absent in disk meta fall through to cached context stats', async () => {
+    writeFileSync(path.join(repoPath, 'a.ts'), 'export const a = 1;\n');
+    runGit(repoPath, 'add', 'a.ts');
+    runGit(repoPath, 'commit', '-m', 'c1');
+    const c1 = runGit(repoPath, 'rev-parse', 'HEAD');
+
+    const oldStats = { files: 77, nodes: 333, processes: 4 };
+    await seedIndexedRepo(repoPath, storagePath, {
+      repoPath,
+      lastCommit: c1,
+      indexedAt: '2024-01-01T00:00:00Z',
+      stats: oldStats,
+    });
+
+    const backend = new LocalBackend();
+    await backend.init();
+
+    // Overwrite disk meta with NO stats (simulating an older/partial file)
+    await saveMeta(storagePath, {
+      repoPath,
+      lastCommit: c1,
+      indexedAt: new Date().toISOString(),
+    });
+
+    const result = await readResource(`gitnexus://repo/test-repo/context`, backend);
+    // Falls back to cached context stats (from registry entry)
+    expect(result).toContain('files: 77');
+    expect(result).toContain('symbols: 333');
+    expect(result).toContain('processes: 4');
+  });
+});
diff --git a/gitnexus/test/unit/resources.test.ts b/gitnexus/test/unit/resources.test.ts
index a0ea2348f..4879c2d14 100644
--- a/gitnexus/test/unit/resources.test.ts
+++ b/gitnexus/test/unit/resources.test.ts
@@ -8,7 +8,7 @@
  * - Error handling for invalid URIs
  * - Resource handlers with mocked backend
  */
-import { describe, it, expect, vi } from 'vitest';
+import { describe, it, expect, vi, beforeEach } from 'vitest';
 import {
   getResourceDefinitions,
   getResourceTemplates,
@@ -16,6 +16,14 @@ import {
   readResource,
 } from '../../src/mcp/resources.js';
 
+// Mock loadMeta so getContextResource doesn't hit the filesystem (#2438 fix).
+// Default: returns null (simulates no on-disk meta — falls back to cached handle).
+const { loadMetaMock } = vi.hoisted(() => ({ loadMetaMock: vi.fn().mockResolvedValue(null) }));
+vi.mock('../../src/storage/repo-manager.js', async (importOriginal) => {
+  const actual = await importOriginal<typeof import('../../src/storage/repo-manager.js')>();
+  return { ...actual, loadMeta: loadMetaMock };
+});
+
 // ─── Minimal mock backend ──────────────────────────────────────────
 
 function createMockBackend(overrides: Partial<Record<string, any>> = {}): any {
@@ -25,6 +33,8 @@ function createMockBackend(overrides: Partial<Record<string, any>> = {}): any {
       overrides.resolvedRepo ?? {
         name: 'test-repo',
         repoPath: '/tmp/test-repo',
+        storagePath: '/tmp/test-repo/.gitnexus',
+        lbugPath: '/tmp/test-repo/.gitnexus/lbug',
         lastCommit: 'abc1234',
       },
     ),
@@ -394,3 +404,124 @@ describe('readResource', () => {
     expect(result).not.toMatch(/gitnexus_/);
   });
 });
+
+// ─── Context resource freshness (#2438) ─────────────────────────────────────
+//
+// After an out-of-process `analyze --index-only` refresh, the RepoHandle cached
+// by LocalBackend is stale (lastCommit and stats come from the registry snapshot
+// taken at init time). getContextResource must read from disk on every call so
+// the staleness banner and stats always reflect the actual on-disk state.
+
+describe('context resource freshness after out-of-process analyze (#2438)', () => {
+  beforeEach(() => {
+    loadMetaMock.mockReset();
+    loadMetaMock.mockResolvedValue(null); // default: no fresh meta
+  });
+
+  const CONTEXT = {
+    projectName: 'test-project',
+    stats: { fileCount: 100, functionCount: 500, communityCount: 3, processCount: 10 },
+  };
+
+  it('uses fresh lastCommit from disk meta for staleness check', async () => {
+    // Simulate: the cached handle has an old commit, but the on-disk meta has
+    // been updated to the current HEAD by an out-of-process analyze.
+    loadMetaMock.mockResolvedValue({
+      repoPath: '/tmp/test-repo',
+      lastCommit: 'fresh-head-commit',
+      indexedAt: new Date().toISOString(),
+      stats: { files: 200, nodes: 1000, processes: 20 },
+    });
+
+    const backend = createMockBackend({
+      resolvedRepo: {
+        name: 'test-project',
+        repoPath: '/tmp/test-repo',
+        storagePath: '/tmp/test-repo/.gitnexus',
+        lbugPath: '/tmp/test-repo/.gitnexus/lbug',
+        lastCommit: 'old-stale-commit', // stale cached value
+      },
+      context: CONTEXT,
+    });
+
+    // loadMeta is called with storagePath, not lbugPath
+    await readResource('gitnexus://repo/test-project/context', backend);
+    expect(loadMetaMock).toHaveBeenCalledWith('/tmp/test-repo/.gitnexus');
+  });
+
+  it('shows fresh stats from disk meta after out-of-process analyze', async () => {
+    // Cached stats are stale (100 files, 500 symbols); disk meta has refreshed stats
+    loadMetaMock.mockResolvedValue({
+      repoPath: '/tmp/test-repo',
+      lastCommit: 'current-head',
+      indexedAt: new Date().toISOString(),
+      stats: { files: 250, nodes: 1500, processes: 25 },
+    });
+
+    const backend = createMockBackend({
+      context: CONTEXT, // stale: fileCount:100, functionCount:500
+    });
+
+    const result = await readResource('gitnexus://repo/test-project/context', backend);
+    // Fresh stats from disk override the cached context stats
+    expect(result).toContain('files: 250');
+    expect(result).toContain('symbols: 1500');
+    expect(result).toContain('processes: 25');
+    // Stale cached values should NOT appear
+    expect(result).not.toContain('files: 100');
+    expect(result).not.toContain('symbols: 500');
+  });
+
+  it('falls back to cached stats when loadMeta returns null', async () => {
+    // loadMeta returns null (e.g. pre-analyze state or missing gitnexus.json)
+    loadMetaMock.mockResolvedValue(null);
+
+    const backend = createMockBackend({ context: CONTEXT });
+    const result = await readResource('gitnexus://repo/test-project/context', backend);
+    // Must still show the cached stats (no crash, no blank output)
+    expect(result).toContain('files: 100');
+    expect(result).toContain('symbols: 500');
+    expect(result).toContain('processes: 10');
+  });
+
+  it('falls back to cached lastCommit when loadMeta throws', async () => {
+    // loadMeta throws (e.g. permissions error)
+    loadMetaMock.mockRejectedValue(new Error('EACCES: permission denied'));
+
+    const backend = createMockBackend({ context: CONTEXT });
+    // Should not throw — falls back gracefully
+    const result = await readResource('gitnexus://repo/test-project/context', backend);
+    expect(result).toContain('test-project');
+    expect(result).toContain('stats:');
+  });
+
+  it('does not show staleness banner when fresh lastCommit matches HEAD', async () => {
+    // After analyze completes, lastCommit in meta equals HEAD → no stale banner.
+    // We simulate this by returning a fresh meta; checkStaleness will be called
+    // with the fresh commit but the /tmp path has no git repo so it returns safe.
+    loadMetaMock.mockResolvedValue({
+      repoPath: '/tmp/test-repo',
+      lastCommit: 'head-after-analyze',
+      indexedAt: new Date().toISOString(),
+      stats: { files: 200, nodes: 1000, processes: 20 },
+    });
+
+    const backend = createMockBackend({
+      resolvedRepo: {
+        name: 'test-project',
+        repoPath: '/tmp/test-repo',
+        storagePath: '/tmp/test-repo/.gitnexus',
+        lbugPath: '/tmp/test-repo/.gitnexus/lbug',
+        lastCommit: 'old-stale-commit', // stale, would show banner if used
+      },
+      context: CONTEXT,
+    });
+
+    const result = await readResource('gitnexus://repo/test-project/context', backend);
+    // With a non-git path checkStaleness errors → no banner even with stale commit.
+    // What matters: the fresh commit was passed to checkStaleness, not the old one.
+    // (The staleness banner itself requires a live git repo, tested in integration.)
+    expect(result).toContain('test-project');
+    expect(result).not.toContain('error:');
+  });
+});