diff --git a/__tests__/cli-affected-paths.test.ts b/__tests__/cli-affected-paths.test.ts
index 88b06cd49..f85d6eba2 100644
--- a/__tests__/cli-affected-paths.test.ts
+++ b/__tests__/cli-affected-paths.test.ts
@@ -18,8 +18,8 @@ import { CodeGraph } from '../src';
 
 const BIN = path.resolve(__dirname, '../dist/bin/codegraph.js');
 
-function affected(cwd: string, arg: string): string[] {
-  const out = execFileSync(process.execPath, [BIN, 'affected', arg, '--quiet', '-p', cwd], {
+function affected(cwd: string, arg: string, extraArgs: string[] = []): string[] {
+  const out = execFileSync(process.execPath, [BIN, 'affected', arg, '--quiet', '-p', cwd, ...extraArgs], {
     encoding: 'utf-8',
     env: { ...process.env, CODEGRAPH_NO_DAEMON: '1', CODEGRAPH_WASM_RELAUNCHED: '1' },
     stdio: ['ignore', 'pipe', 'pipe'],
@@ -43,6 +43,13 @@ describe('codegraph affected — input path normalization (#825)', () => {
       path.join(tempDir, 'src/helper.test.ts'),
       "import { helper } from './helper';\ntest('t', () => helper());\n",
     );
+    fs.mkdirSync(path.join(tempDir, 'python'));
+    fs.mkdirSync(path.join(tempDir, 'tests'));
+    fs.writeFileSync(path.join(tempDir, 'python/math_utils.py'), 'def add_one(value):\n    return value + 1\n');
+    fs.writeFileSync(
+      path.join(tempDir, 'tests/test_math_utils.py'),
+      'from python.math_utils import add_one\n\ndef test_add_one():\n    assert add_one(1) == 2\n',
+    );
     const cg = CodeGraph.initSync(tempDir);
     await cg.indexAll();
     cg.close();
@@ -60,4 +67,13 @@ describe('codegraph affected — input path normalization (#825)', () => {
     expect(affected(tempDir, './src/util.ts')).toEqual(expected);
     expect(affected(tempDir, path.join(tempDir, 'src/util.ts'))).toEqual(expected);
   });
+
+  it('recognizes pytest files in a root-level tests directory', () => {
+    expect(affected(tempDir, 'python/math_utils.py')).toEqual(['tests/test_math_utils.py']);
+  });
+
+  it('treats globstar as zero or more directories in custom filters', () => {
+    expect(affected(tempDir, 'python/math_utils.py', ['--filter', 'tests/**/*.py']))
+      .toEqual(['tests/test_math_utils.py']);
+  });
 });
diff --git a/src/bin/codegraph.ts b/src/bin/codegraph.ts
index 4d85e204f..fe3dea2c7 100644
--- a/src/bin/codegraph.ts
+++ b/src/bin/codegraph.ts
@@ -33,6 +33,8 @@ import * as path from 'path';
 import * as fs from 'fs';
 import { getCodeGraphDir, isInitialized, unsafeIndexRootReason, findNearestCodeGraphRoot, planFrontload, hasStructuralKeyword, extractCodeTokens } from '../directory';
 import { extractProseCandidates } from '../search/identifier-segments';
+import { isTestFile as isDefaultTestFile } from '../search/query-utils';
+import picomatch from 'picomatch';
 import { detectWorktreeIndexMismatch, worktreeMismatchWarning } from '../sync/worktree';
 import { createShimmerProgress } from '../ui/shimmer-progress';
 import { getGlyphs } from '../ui/glyphs';
@@ -2090,31 +2092,11 @@ program
       const cg = await CodeGraph.open(projectPath);
       const maxDepth = parseInt(options.depth || '5', 10);
 
-      // Common test file patterns
-      const defaultTestPatterns = [
-        /\.spec\./,
-        /\.test\./,
-        /\/__tests__\//,
-        /\/tests?\//,
-        /\/e2e\//,
-        /\/spec\//,
-      ];
-
-      // Custom filter pattern
-      let customFilter: RegExp | null = null;
-      if (options.filter) {
-        // Convert glob to regex: ** → .+, * → [^/]*, . → \.
-        const regex = options.filter
-          .replace(/[+[\]{}()^$|\\]/g, '\\$&')
-          .replace(/\./g, '\\.')
-          .replace(/\*\*/g, '.+')
-          .replace(/\*/g, '[^/]*');
-        customFilter = new RegExp(regex);
-      }
+      const customFilter = options.filter ? picomatch(options.filter) : null;
 
-      function isTestFile(filePath: string): boolean {
-        if (customFilter) return customFilter.test(filePath);
-        return defaultTestPatterns.some(p => p.test(filePath));
+      function matchesTestFile(filePath: string): boolean {
+        if (customFilter) return customFilter(filePath);
+        return isDefaultTestFile(filePath);
       }
 
       // BFS to find all transitive dependents of changed files, filtered to test files
@@ -2123,7 +2105,7 @@ program
 
       for (const file of changedFiles) {
         // If the changed file is itself a test file, include it
-        if (isTestFile(file)) {
+        if (matchesTestFile(file)) {
           affectedTests.add(file);
           continue;
         }
@@ -2143,7 +2125,7 @@ program
             visited.add(dep);
             allDependents.add(dep);
 
-            if (isTestFile(dep)) {
+            if (matchesTestFile(dep)) {
               affectedTests.add(dep);
             } else {
               queue.push({ file: dep, depth: current.depth + 1 });