diff --git a/gitnexus/src/mcp/local/local-backend.ts b/gitnexus/src/mcp/local/local-backend.ts
index ec4872cdd..d4b3ea063 100644
--- a/gitnexus/src/mcp/local/local-backend.ts
+++ b/gitnexus/src/mcp/local/local-backend.ts
@@ -799,6 +799,21 @@ export function resolveWorktreeCwd(repoPath: string, launchCwd: string): string
   return repoPath;
 }
 
+export function buildDetectChangesDiffArgs(scope: string, baseRef?: string): string[] | null {
+  const args = ['diff', '--ignore-cr-at-eol'];
+  switch (scope) {
+    case 'staged':
+      return [...args, '--staged', '-U0'];
+    case 'all':
+      return [...args, 'HEAD', '-U0'];
+    case 'compare':
+      return baseRef ? [...args, baseRef, '-U0'] : null;
+    case 'unstaged':
+    default:
+      return [...args, '-U0'];
+  }
+}
+
 /**
  * Length of the path-derived suffix appended to a colliding repo id.
  * Exported so tests can pin the suffix shape without re-deriving the
@@ -4917,24 +4932,10 @@ export class LocalBackend {
     const scope = params.scope || 'unstaged';
     const { execFileSync } = await import('child_process');
 
-    // Build git diff args based on scope (using execFileSync to avoid shell injection)
-    let diffArgs: string[];
-    switch (scope) {
-      case 'staged':
-        diffArgs = ['diff', '--staged', '-U0'];
-        break;
-      case 'all':
-        diffArgs = ['diff', 'HEAD', '-U0'];
-        break;
-      case 'compare':
-        if (!params.base_ref) return { error: 'base_ref is required for "compare" scope' };
-        diffArgs = ['diff', params.base_ref, '-U0'];
-        break;
-      case 'unstaged':
-      default:
-        diffArgs = ['diff', '-U0'];
-        break;
-    }
+    // Ignore CR-only EOL differences, while preserving meaningful whitespace changes.
+    // execFileSync receives an argv array, so refs never pass through a shell.
+    const diffArgs = buildDetectChangesDiffArgs(scope, params.base_ref);
+    if (!diffArgs) return { error: 'base_ref is required for "compare" scope' };
 
     let diffOutput: string;
     try {
diff --git a/gitnexus/test/unit/detect-changes-eol.test.ts b/gitnexus/test/unit/detect-changes-eol.test.ts
new file mode 100644
index 000000000..52a56c35b
--- /dev/null
+++ b/gitnexus/test/unit/detect-changes-eol.test.ts
@@ -0,0 +1,53 @@
+import { execFileSync } from 'node:child_process';
+import { mkdtempSync, rmSync, writeFileSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import path from 'node:path';
+import { describe, expect, it } from 'vitest';
+import { buildDetectChangesDiffArgs } from '../../src/mcp/local/local-backend.js';
+
+describe('detect_changes EOL filtering', () => {
+  it.each([
+    ['unstaged', undefined, ['diff', '--ignore-cr-at-eol', '-U0']],
+    ['staged', undefined, ['diff', '--ignore-cr-at-eol', '--staged', '-U0']],
+    ['all', undefined, ['diff', '--ignore-cr-at-eol', 'HEAD', '-U0']],
+    ['compare', 'main', ['diff', '--ignore-cr-at-eol', 'main', '-U0']],
+  ])('adds the EOL guard for %s scope', (scope, baseRef, expected) => {
+    expect(buildDetectChangesDiffArgs(scope, baseRef)).toEqual(expected);
+  });
+
+  it('requires a base ref for compare scope', () => {
+    expect(buildDetectChangesDiffArgs('compare')).toBeNull();
+  });
+
+  it('suppresses CRLF-only changes but retains other whitespace changes', () => {
+    const repoDir = mkdtempSync(path.join(tmpdir(), 'gitnexus-detect-eol-'));
+    try {
+      execFileSync('git', ['init', '-q'], { cwd: repoDir });
+      execFileSync('git', ['config', 'user.email', 'test@example.com'], { cwd: repoDir });
+      execFileSync('git', ['config', 'user.name', 'Test'], { cwd: repoDir });
+      writeFileSync(path.join(repoDir, 'sample.ts'), 'const first = 1;\r\nconst second = 2;\r\n');
+      execFileSync('git', ['add', 'sample.ts'], { cwd: repoDir });
+      execFileSync('git', ['commit', '-q', '-m', 'initial'], { cwd: repoDir });
+
+      writeFileSync(path.join(repoDir, 'sample.ts'), 'const first = 1;\nconst second = 2;\n');
+      const diffArgs = buildDetectChangesDiffArgs('unstaged');
+      if (!diffArgs) throw new Error('unstaged scope must produce git diff arguments');
+      expect(
+        execFileSync('git', diffArgs, {
+          cwd: repoDir,
+          encoding: 'utf8',
+        }),
+      ).toBe('');
+
+      writeFileSync(path.join(repoDir, 'sample.ts'), 'const first = 1;\n  const second = 2;\n');
+      expect(
+        execFileSync('git', diffArgs, {
+          cwd: repoDir,
+          encoding: 'utf8',
+        }),
+      ).toContain('+  const second = 2;');
+    } finally {
+      rmSync(repoDir, { recursive: true, force: true });
+    }
+  });
+});