diff --git a/packages/cli/src/ui/hooks/atCommandProcessor.test.ts b/packages/cli/src/ui/hooks/atCommandProcessor.test.ts
index 08631634..efe15c64 100644
--- a/packages/cli/src/ui/hooks/atCommandProcessor.test.ts
+++ b/packages/cli/src/ui/hooks/atCommandProcessor.test.ts
@@ -90,7 +90,7 @@ describe('handleAtCommand', () => {
     // Mock FileDiscoveryService
     mockFileDiscoveryService = {
       initialize: vi.fn(),
-      shouldGitIgnoreFile: vi.fn(() => false),
+      shouldIgnoreFile: vi.fn(() => false),
       filterFiles: vi.fn((files) => files),
       getIgnoreInfo: vi.fn(() => ({ gitIgnored: [] })),
       isGitRepository: vi.fn(() => true),
@@ -171,7 +171,7 @@ describe('handleAtCommand', () => {
       125,
     );
     expect(mockReadManyFilesExecute).toHaveBeenCalledWith(
-      { paths: [filePath], respectGitIgnore: true },
+      { paths: [filePath], respect_git_ignore: true },
       abortController.signal,
     );
     expect(mockAddItem).toHaveBeenCalledWith(
@@ -217,7 +217,7 @@ describe('handleAtCommand', () => {
       126,
     );
     expect(mockReadManyFilesExecute).toHaveBeenCalledWith(
-      { paths: [resolvedGlob], respectGitIgnore: true },
+      { paths: [resolvedGlob], respect_git_ignore: true },
       abortController.signal,
     );
     expect(mockOnDebugMessage).toHaveBeenCalledWith(
@@ -318,7 +318,7 @@ describe('handleAtCommand', () => {
       signal: abortController.signal,
     });
     expect(mockReadManyFilesExecute).toHaveBeenCalledWith(
-      { paths: [unescapedPath], respectGitIgnore: true },
+      { paths: [unescapedPath], respect_git_ignore: true },
       abortController.signal,
     );
   });
@@ -347,7 +347,7 @@ describe('handleAtCommand', () => {
       signal: abortController.signal,
     });
     expect(mockReadManyFilesExecute).toHaveBeenCalledWith(
-      { paths: [file1, file2], respectGitIgnore: true },
+      { paths: [file1, file2], respect_git_ignore: true },
       abortController.signal,
     );
     expect(result.processedQuery).toEqual([
@@ -389,7 +389,7 @@ describe('handleAtCommand', () => {
       signal: abortController.signal,
     });
     expect(mockReadManyFilesExecute).toHaveBeenCalledWith(
-      { paths: [file1, file2], respectGitIgnore: true },
+      { paths: [file1, file2], respect_git_ignore: true },
       abortController.signal,
     );
     expect(result.processedQuery).toEqual([
@@ -454,7 +454,7 @@ describe('handleAtCommand', () => {
     });
 
     expect(mockReadManyFilesExecute).toHaveBeenCalledWith(
-      { paths: [file1, resolvedFile2], respectGitIgnore: true },
+      { paths: [file1, resolvedFile2], respect_git_ignore: true },
       abortController.signal,
     );
     expect(result.processedQuery).toEqual([
@@ -556,7 +556,7 @@ describe('handleAtCommand', () => {
       // If the mock is simpler, it might use queryPath if stat(queryPath) succeeds.
       // The most important part is that *some* version of the path that leads to the content is used.
       // Let's assume it uses the path from the query if stat confirms it exists (even if different case on disk)
-      { paths: [queryPath], respectGitIgnore: true },
+      { paths: [queryPath], respect_git_ignore: true },
       abortController.signal,
     );
     expect(mockAddItem).toHaveBeenCalledWith(
@@ -582,8 +582,9 @@ describe('handleAtCommand', () => {
       const query = `@${gitIgnoredFile}`;
 
       // Mock the file discovery service to report this file as git-ignored
-      mockFileDiscoveryService.shouldGitIgnoreFile.mockImplementation(
-        (path: string) => path === gitIgnoredFile,
+      mockFileDiscoveryService.shouldIgnoreFile.mockImplementation(
+        (path: string, options?: { respectGitIgnore?: boolean }) =>
+          path === gitIgnoredFile && options?.respectGitIgnore !== false,
       );
 
       const result = await handleAtCommand({
@@ -595,8 +596,9 @@ describe('handleAtCommand', () => {
         signal: abortController.signal,
       });
 
-      expect(mockFileDiscoveryService.shouldGitIgnoreFile).toHaveBeenCalledWith(
+      expect(mockFileDiscoveryService.shouldIgnoreFile).toHaveBeenCalledWith(
         gitIgnoredFile,
+        { respectGitIgnore: true },
       );
       expect(mockOnDebugMessage).toHaveBeenCalledWith(
         `Path ${gitIgnoredFile} is git-ignored and will be skipped.`,
@@ -614,7 +616,7 @@ describe('handleAtCommand', () => {
       const query = `@${validFile}`;
       const fileContent = 'console.log("Hello world");';
 
-      mockFileDiscoveryService.shouldGitIgnoreFile.mockReturnValue(false);
+      mockFileDiscoveryService.shouldIgnoreFile.mockReturnValue(false);
       mockReadManyFilesExecute.mockResolvedValue({
         llmContent: [`--- ${validFile} ---\n\n${fileContent}\n\n`],
         returnDisplay: 'Read 1 file.',
@@ -629,11 +631,12 @@ describe('handleAtCommand', () => {
         signal: abortController.signal,
       });
 
-      expect(mockFileDiscoveryService.shouldGitIgnoreFile).toHaveBeenCalledWith(
+      expect(mockFileDiscoveryService.shouldIgnoreFile).toHaveBeenCalledWith(
         validFile,
+        { respectGitIgnore: true },
       );
       expect(mockReadManyFilesExecute).toHaveBeenCalledWith(
-        { paths: [validFile], respectGitIgnore: true },
+        { paths: [validFile], respect_git_ignore: true },
         abortController.signal,
       );
       expect(result.processedQuery).toEqual([
@@ -652,8 +655,9 @@ describe('handleAtCommand', () => {
       const query = `@${validFile} @${gitIgnoredFile}`;
       const fileContent = '# Project README';
 
-      mockFileDiscoveryService.shouldGitIgnoreFile.mockImplementation(
-        (path: string) => path === gitIgnoredFile,
+      mockFileDiscoveryService.shouldIgnoreFile.mockImplementation(
+        (path: string, options?: { respectGitIgnore?: boolean }) =>
+          path === gitIgnoredFile && options?.respectGitIgnore !== false,
       );
       mockReadManyFilesExecute.mockResolvedValue({
         llmContent: [`--- ${validFile} ---\n\n${fileContent}\n\n`],
@@ -669,11 +673,13 @@ describe('handleAtCommand', () => {
         signal: abortController.signal,
       });
 
-      expect(mockFileDiscoveryService.shouldGitIgnoreFile).toHaveBeenCalledWith(
+      expect(mockFileDiscoveryService.shouldIgnoreFile).toHaveBeenCalledWith(
         validFile,
+        { respectGitIgnore: true },
       );
-      expect(mockFileDiscoveryService.shouldGitIgnoreFile).toHaveBeenCalledWith(
+      expect(mockFileDiscoveryService.shouldIgnoreFile).toHaveBeenCalledWith(
         gitIgnoredFile,
+        { respectGitIgnore: true },
       );
       expect(mockOnDebugMessage).toHaveBeenCalledWith(
         `Path ${gitIgnoredFile} is git-ignored and will be skipped.`,
@@ -682,7 +688,7 @@ describe('handleAtCommand', () => {
         'Ignored 1 git-ignored files: .env',
       );
       expect(mockReadManyFilesExecute).toHaveBeenCalledWith(
-        { paths: [validFile], respectGitIgnore: true },
+        { paths: [validFile], respect_git_ignore: true },
         abortController.signal,
       );
       expect(result.processedQuery).toEqual([
@@ -699,7 +705,7 @@ describe('handleAtCommand', () => {
       const gitFile = '.git/config';
       const query = `@${gitFile}`;
 
-      mockFileDiscoveryService.shouldGitIgnoreFile.mockReturnValue(true);
+      mockFileDiscoveryService.shouldIgnoreFile.mockReturnValue(true);
 
       const result = await handleAtCommand({
         query,
@@ -710,8 +716,9 @@ describe('handleAtCommand', () => {
         signal: abortController.signal,
       });
 
-      expect(mockFileDiscoveryService.shouldGitIgnoreFile).toHaveBeenCalledWith(
+      expect(mockFileDiscoveryService.shouldIgnoreFile).toHaveBeenCalledWith(
         gitFile,
+        { respectGitIgnore: true },
       );
       expect(mockOnDebugMessage).toHaveBeenCalledWith(
         `Path ${gitFile} is git-ignored and will be skipped.`,
diff --git a/packages/cli/src/ui/hooks/atCommandProcessor.ts b/packages/cli/src/ui/hooks/atCommandProcessor.ts
index 80393ef2..7fe68f10 100644
--- a/packages/cli/src/ui/hooks/atCommandProcessor.ts
+++ b/packages/cli/src/ui/hooks/atCommandProcessor.ts
@@ -181,12 +181,10 @@ export async function handleAtCommand({
       return { processedQuery: null, shouldProceed: false };
     }
 
-    // Check if path should be ignored by git
-    if (fileDiscovery.shouldGitIgnoreFile(pathName)) {
-      const reason = respectGitIgnore
-        ? 'git-ignored and will be skipped'
-        : 'ignored by custom patterns';
-      onDebugMessage(`Path ${pathName} is ${reason}.`);
+    // Check if path should be ignored based on filtering options
+    if (fileDiscovery.shouldIgnoreFile(pathName, { respectGitIgnore })) {
+      const reason = respectGitIgnore ? 'git-ignored' : 'custom-ignored';
+      onDebugMessage(`Path ${pathName} is ${reason} and will be skipped.`);
       ignoredPaths.push(pathName);
       continue;
     }
@@ -349,7 +347,7 @@ export async function handleAtCommand({
 
   const toolArgs = {
     paths: pathSpecsToRead,
-    respectGitIgnore, // Use configuration setting
+    respect_git_ignore: respectGitIgnore, // Use configuration setting
   };
   let toolCallDisplay: IndividualToolCallDisplay;
 
diff --git a/packages/cli/src/ui/hooks/useCompletion.integration.test.ts b/packages/cli/src/ui/hooks/useCompletion.integration.test.ts
index 6a178fb1..f5864a58 100644
--- a/packages/cli/src/ui/hooks/useCompletion.integration.test.ts
+++ b/packages/cli/src/ui/hooks/useCompletion.integration.test.ts
@@ -41,7 +41,10 @@ describe('useCompletion git-aware filtering integration', () => {
   beforeEach(() => {
     mockFileDiscoveryService = {
       shouldGitIgnoreFile: vi.fn(),
+      shouldGeminiIgnoreFile: vi.fn(),
+      shouldIgnoreFile: vi.fn(),
       filterFiles: vi.fn(),
+      getGeminiIgnorePatterns: vi.fn(() => []),
     };
 
     mockConfig = {
@@ -68,6 +71,14 @@ describe('useCompletion git-aware filtering integration', () => {
     mockFileDiscoveryService.shouldGitIgnoreFile.mockImplementation(
       (path: string) => path.includes('dist'),
     );
+    mockFileDiscoveryService.shouldIgnoreFile.mockImplementation(
+      (path: string, options) => {
+        if (options?.respectGitIgnore !== false) {
+          return mockFileDiscoveryService.shouldGitIgnoreFile(path);
+        }
+        return false;
+      },
+    );
 
     const { result } = renderHook(() =>
       useCompletion('@d', testCwd, true, slashCommands, mockConfig),
@@ -102,6 +113,14 @@ describe('useCompletion git-aware filtering integration', () => {
         path.includes('dist') ||
         path.includes('.env'),
     );
+    mockFileDiscoveryService.shouldIgnoreFile.mockImplementation(
+      (path: string, options) => {
+        if (options?.respectGitIgnore !== false) {
+          return mockFileDiscoveryService.shouldGitIgnoreFile(path);
+        }
+        return false;
+      },
+    );
 
     const { result } = renderHook(() =>
       useCompletion('@', testCwd, true, slashCommands, mockConfig),
@@ -153,6 +172,14 @@ describe('useCompletion git-aware filtering integration', () => {
     mockFileDiscoveryService.shouldGitIgnoreFile.mockImplementation(
       (path: string) => path.includes('node_modules') || path.includes('temp'),
     );
+    mockFileDiscoveryService.shouldIgnoreFile.mockImplementation(
+      (path: string, options) => {
+        if (options?.respectGitIgnore !== false) {
+          return mockFileDiscoveryService.shouldGitIgnoreFile(path);
+        }
+        return false;
+      },
+    );
 
     const { result } = renderHook(() =>
       useCompletion('@t', testCwd, true, slashCommands, mockConfig),
@@ -261,6 +288,14 @@ describe('useCompletion git-aware filtering integration', () => {
     mockFileDiscoveryService.shouldGitIgnoreFile.mockImplementation(
       (path: string) => path.includes('.log'),
     );
+    mockFileDiscoveryService.shouldIgnoreFile.mockImplementation(
+      (path: string, options) => {
+        if (options?.respectGitIgnore !== false) {
+          return mockFileDiscoveryService.shouldGitIgnoreFile(path);
+        }
+        return false;
+      },
+    );
 
     const { result } = renderHook(() =>
       useCompletion('@src/comp', testCwd, true, slashCommands, mockConfig),
diff --git a/packages/cli/src/ui/hooks/useCompletion.ts b/packages/cli/src/ui/hooks/useCompletion.ts
index 27a1c708..fd826c92 100644
--- a/packages/cli/src/ui/hooks/useCompletion.ts
+++ b/packages/cli/src/ui/hooks/useCompletion.ts
@@ -217,7 +217,11 @@ export function useCompletion(
     const findFilesRecursively = async (
       startDir: string,
       searchPrefix: string,
-      fileDiscovery: { shouldGitIgnoreFile: (path: string) => boolean } | null,
+      fileDiscovery: FileDiscoveryService | null,
+      filterOptions: {
+        respectGitIgnore?: boolean;
+        respectGeminiIgnore?: boolean;
+      },
       currentRelativePath = '',
       depth = 0,
       maxDepth = 10, // Limit recursion depth
@@ -245,10 +249,10 @@ export function useCompletion(
             continue;
           }
 
-          // Check if this entry should be ignored by git-aware filtering
+          // Check if this entry should be ignored by filtering options
           if (
             fileDiscovery &&
-            fileDiscovery.shouldGitIgnoreFile(entryPathFromRoot)
+            fileDiscovery.shouldIgnoreFile(entryPathFromRoot, filterOptions)
           ) {
             continue;
           }
@@ -272,6 +276,7 @@ export function useCompletion(
                   path.join(startDir, entry.name),
                   searchPrefix, // Pass original searchPrefix for recursive calls
                   fileDiscovery,
+                  filterOptions,
                   entryPathRelative,
                   depth + 1,
                   maxDepth,
@@ -290,6 +295,10 @@ export function useCompletion(
     const findFilesWithGlob = async (
       searchPrefix: string,
       fileDiscoveryService: FileDiscoveryService,
+      filterOptions: {
+        respectGitIgnore?: boolean;
+        respectGeminiIgnore?: boolean;
+      },
       maxResults = 50,
     ): Promise<Suggestion[]> => {
       const globPattern = `**/${searchPrefix}*`;
@@ -309,7 +318,10 @@ export function useCompletion(
         })
         .filter((s) => {
           if (fileDiscoveryService) {
-            return !fileDiscoveryService.shouldGitIgnoreFile(s.label); // relative path
+            return !fileDiscoveryService.shouldIgnoreFile(
+              s.label,
+              filterOptions,
+            ); // relative path
           }
           return true;
         })
@@ -325,6 +337,10 @@ export function useCompletion(
       const fileDiscoveryService = config ? config.getFileService() : null;
       const enableRecursiveSearch =
         config?.getEnableRecursiveFileSearch() ?? true;
+      const filterOptions = {
+        respectGitIgnore: config?.getFileFilteringRespectGitIgnore() ?? true,
+        respectGeminiIgnore: true,
+      };
 
       try {
         // If there's no slash, or it's the root, do a recursive search from cwd
@@ -337,12 +353,14 @@ export function useCompletion(
             fetchedSuggestions = await findFilesWithGlob(
               prefix,
               fileDiscoveryService,
+              filterOptions,
             );
           } else {
             fetchedSuggestions = await findFilesRecursively(
               cwd,
               prefix,
               fileDiscoveryService,
+              filterOptions,
             );
           }
         } else {
@@ -367,7 +385,7 @@ export function useCompletion(
             );
             if (
               fileDiscoveryService &&
-              fileDiscoveryService.shouldGitIgnoreFile(relativePath)
+              fileDiscoveryService.shouldIgnoreFile(relativePath, filterOptions)
             ) {
               continue;
             }
diff --git a/packages/core/src/services/fileDiscoveryService.ts b/packages/core/src/services/fileDiscoveryService.ts
index 984f3f53..22092813 100644
--- a/packages/core/src/services/fileDiscoveryService.ts
+++ b/packages/core/src/services/fileDiscoveryService.ts
@@ -84,6 +84,24 @@ export class FileDiscoveryService {
     return false;
   }
 
+  /**
+   * Unified method to check if a file should be ignored based on filtering options
+   */
+  shouldIgnoreFile(
+    filePath: string,
+    options: FilterFilesOptions = {},
+  ): boolean {
+    const { respectGitIgnore = true, respectGeminiIgnore = true } = options;
+
+    if (respectGitIgnore && this.shouldGitIgnoreFile(filePath)) {
+      return true;
+    }
+    if (respectGeminiIgnore && this.shouldGeminiIgnoreFile(filePath)) {
+      return true;
+    }
+    return false;
+  }
+
   /**
    * Returns loaded patterns from .geminiignore
    */