diff --git a/src/core/file/fileSearch.ts b/src/core/file/fileSearch.ts
index 492af837e..7073e5337 100644
--- a/src/core/file/fileSearch.ts
+++ b/src/core/file/fileSearch.ts
@@ -330,6 +330,9 @@ export const getIgnoreFilePatterns = async (config: RepomixConfigMerged): Promis
   //
   // .gitignore files are handled by globby's gitignore option (not ignoreFiles)
   // to properly respect parent directory .gitignore files, matching Git's behavior.
+  //
+  // These ignore file patterns are always applied regardless of whether customPatterns
+  // is defined in the config. Both sources are merged by globby at the file search level.
 
   if (config.ignore.useDotIgnore) {
     ignoreFilePatterns.push('**/.ignore');
diff --git a/tests/config/configLoad.test.ts b/tests/config/configLoad.test.ts
index aa221e7b4..7e92e86ae 100644
--- a/tests/config/configLoad.test.ts
+++ b/tests/config/configLoad.test.ts
@@ -351,5 +351,54 @@ describe('configLoad', () => {
       const merged = mergeConfigs(process.cwd(), {}, { skillGenerate: 'from-cli' });
       expect(merged.skillGenerate).toBe('from-cli');
     });
+
+    // Regression tests for #959: .ignore file should work when customPatterns is defined
+    test('should preserve useDotIgnore default when only customPatterns is defined in fileConfig', () => {
+      const fileConfig: RepomixConfigFile = {
+        ignore: {
+          customPatterns: ['bin/'],
+        },
+      };
+      const cliConfig: RepomixConfigCli = {};
+      const merged = mergeConfigs(process.cwd(), fileConfig, cliConfig);
+
+      expect(merged.ignore.useDotIgnore).toBe(true);
+      expect(merged.ignore.useGitignore).toBe(true);
+      expect(merged.ignore.useDefaultPatterns).toBe(true);
+      expect(merged.ignore.customPatterns).toContain('bin/');
+    });
+
+    test('should preserve all ignore boolean flags when customPatterns is defined in both sources', () => {
+      const fileConfig: RepomixConfigFile = {
+        ignore: {
+          customPatterns: ['from-file/'],
+        },
+      };
+      const cliConfig: RepomixConfigCli = {
+        ignore: {
+          customPatterns: ['from-cli/'],
+        },
+      };
+      const merged = mergeConfigs(process.cwd(), fileConfig, cliConfig);
+
+      expect(merged.ignore.useDotIgnore).toBe(true);
+      expect(merged.ignore.useGitignore).toBe(true);
+      expect(merged.ignore.useDefaultPatterns).toBe(true);
+      expect(merged.ignore.customPatterns).toEqual(['from-file/', 'from-cli/']);
+    });
+
+    test('should allow explicitly disabling useDotIgnore alongside customPatterns', () => {
+      const fileConfig: RepomixConfigFile = {
+        ignore: {
+          useDotIgnore: false,
+          customPatterns: ['bin/'],
+        },
+      };
+      const cliConfig: RepomixConfigCli = {};
+      const merged = mergeConfigs(process.cwd(), fileConfig, cliConfig);
+
+      expect(merged.ignore.useDotIgnore).toBe(false);
+      expect(merged.ignore.customPatterns).toContain('bin/');
+    });
   });
 });
diff --git a/tests/core/file/fileSearch.ignore.integration.test.ts b/tests/core/file/fileSearch.ignore.integration.test.ts
new file mode 100644
index 000000000..1f6280229
--- /dev/null
+++ b/tests/core/file/fileSearch.ignore.integration.test.ts
@@ -0,0 +1,157 @@
+import * as fs from 'node:fs/promises';
+import os from 'node:os';
+import * as path from 'node:path';
+import { afterEach, beforeEach, describe, expect, test } from 'vitest';
+import { mergeConfigs } from '../../../src/config/configLoad.js';
+import type { RepomixConfigFile } from '../../../src/config/configSchema.js';
+import { searchFiles } from '../../../src/core/file/fileSearch.js';
+import { createMockConfig } from '../../testing/testUtils.js';
+
+/**
+ * Integration tests for .ignore file behavior when customPatterns is defined.
+ * Regression tests for issue #959.
+ *
+ * These tests use real file system operations to verify that all ignore sources
+ * (.ignore, .repomixignore, customPatterns) are properly merged and applied
+ * together, regardless of which sources are configured.
+ */
+describe('fileSearch - .ignore integration with customPatterns (#959)', () => {
+  let tempDir: string;
+
+  beforeEach(async () => {
+    tempDir = await fs.mkdtemp(path.join(os.tmpdir(), 'repomix-959-'));
+  });
+
+  afterEach(async () => {
+    await fs.rm(tempDir, { recursive: true, force: true });
+  });
+
+  test('should respect .ignore file when customPatterns is defined in config', async () => {
+    // Setup: exact scenario from issue #959
+    await fs.mkdir(path.join(tempDir, 'bin'), { recursive: true });
+    await fs.mkdir(path.join(tempDir, 'spec', 'data'), { recursive: true });
+    await fs.mkdir(path.join(tempDir, 'src'), { recursive: true });
+    await fs.writeFile(path.join(tempDir, 'bin', 'test.sh'), 'bin content');
+    await fs.writeFile(path.join(tempDir, 'spec', 'data', 'test.txt'), 'test content');
+    await fs.writeFile(path.join(tempDir, 'src', 'main.js'), 'main content');
+    await fs.writeFile(path.join(tempDir, '.ignore'), 'spec/data/\n');
+
+    // Simulate: config file has { ignore: { customPatterns: ["bin/"] } }
+    const fileConfig: RepomixConfigFile = {
+      ignore: { customPatterns: ['bin/'] },
+    };
+    const config = mergeConfigs(tempDir, fileConfig, {});
+    const testConfig = { ...config, ignore: { ...config.ignore, useGitignore: false, useDefaultPatterns: false } };
+
+    const result = await searchFiles(tempDir, testConfig);
+
+    // Both bin/ (from customPatterns) and spec/data/ (from .ignore) should be excluded
+    expect(result.filePaths).not.toContain('bin/test.sh');
+    expect(result.filePaths).not.toContain('spec/data/test.txt');
+    expect(result.filePaths).toContain('src/main.js');
+  });
+
+  test('should respect .ignore file when customPatterns is empty', async () => {
+    await fs.mkdir(path.join(tempDir, 'spec', 'data'), { recursive: true });
+    await fs.mkdir(path.join(tempDir, 'src'), { recursive: true });
+    await fs.writeFile(path.join(tempDir, 'spec', 'data', 'test.txt'), 'test content');
+    await fs.writeFile(path.join(tempDir, 'src', 'main.js'), 'main content');
+    await fs.writeFile(path.join(tempDir, '.ignore'), 'spec/data/\n');
+
+    const config = createMockConfig({
+      cwd: tempDir,
+      ignore: {
+        useGitignore: false,
+        useDotIgnore: true,
+        useDefaultPatterns: false,
+        customPatterns: [],
+      },
+    });
+
+    const result = await searchFiles(tempDir, config);
+
+    expect(result.filePaths).not.toContain('spec/data/test.txt');
+    expect(result.filePaths).toContain('src/main.js');
+  });
+
+  test('should not use .ignore when useDotIgnore is false', async () => {
+    await fs.mkdir(path.join(tempDir, 'spec', 'data'), { recursive: true });
+    await fs.mkdir(path.join(tempDir, 'src'), { recursive: true });
+    await fs.writeFile(path.join(tempDir, 'spec', 'data', 'test.txt'), 'test content');
+    await fs.writeFile(path.join(tempDir, 'src', 'main.js'), 'main content');
+    await fs.writeFile(path.join(tempDir, '.ignore'), 'spec/data/\n');
+
+    const config = createMockConfig({
+      cwd: tempDir,
+      ignore: {
+        useGitignore: false,
+        useDotIgnore: false,
+        useDefaultPatterns: false,
+        customPatterns: [],
+      },
+    });
+
+    const result = await searchFiles(tempDir, config);
+
+    // .ignore should NOT be respected when useDotIgnore is false
+    expect(result.filePaths).toContain('spec/data/test.txt');
+    expect(result.filePaths).toContain('src/main.js');
+  });
+
+  test('should merge all ignore sources together', async () => {
+    await fs.mkdir(path.join(tempDir, 'dist'), { recursive: true });
+    await fs.mkdir(path.join(tempDir, 'tmp'), { recursive: true });
+    await fs.mkdir(path.join(tempDir, 'vendor'), { recursive: true });
+    await fs.mkdir(path.join(tempDir, 'src'), { recursive: true });
+    await fs.writeFile(path.join(tempDir, 'dist', 'bundle.js'), 'dist');
+    await fs.writeFile(path.join(tempDir, 'tmp', 'cache.dat'), 'tmp');
+    await fs.writeFile(path.join(tempDir, 'vendor', 'lib.js'), 'vendor');
+    await fs.writeFile(path.join(tempDir, 'src', 'index.js'), 'src');
+    await fs.writeFile(path.join(tempDir, '.ignore'), 'dist/\n');
+    await fs.writeFile(path.join(tempDir, '.repomixignore'), 'tmp/\n');
+
+    const config = createMockConfig({
+      cwd: tempDir,
+      ignore: {
+        useGitignore: false,
+        useDotIgnore: true,
+        useDefaultPatterns: false,
+        customPatterns: ['vendor/'],
+      },
+    });
+
+    const result = await searchFiles(tempDir, config);
+
+    // All three ignore sources should be merged
+    expect(result.filePaths).not.toContain('dist/bundle.js');
+    expect(result.filePaths).not.toContain('tmp/cache.dat');
+    expect(result.filePaths).not.toContain('vendor/lib.js');
+    expect(result.filePaths).toContain('src/index.js');
+  });
+
+  test('should respect .ignore in subdirectory when customPatterns is defined', async () => {
+    await fs.mkdir(path.join(tempDir, 'src', 'generated'), { recursive: true });
+    await fs.mkdir(path.join(tempDir, 'bin'), { recursive: true });
+    await fs.writeFile(path.join(tempDir, 'src', 'app.js'), 'normal');
+    await fs.writeFile(path.join(tempDir, 'src', 'generated', 'output.js'), 'generated');
+    await fs.writeFile(path.join(tempDir, 'bin', 'run.sh'), 'bin');
+    // Subdirectory .ignore file
+    await fs.writeFile(path.join(tempDir, 'src', '.ignore'), 'generated/\n');
+
+    const config = createMockConfig({
+      cwd: tempDir,
+      ignore: {
+        useGitignore: false,
+        useDotIgnore: true,
+        useDefaultPatterns: false,
+        customPatterns: ['bin/'],
+      },
+    });
+
+    const result = await searchFiles(tempDir, config);
+
+    expect(result.filePaths).not.toContain('bin/run.sh');
+    expect(result.filePaths).not.toContain('src/generated/output.js');
+    expect(result.filePaths).toContain('src/app.js');
+  });
+});