diff --git a/src/auto_commit_service/git/__pycache__/operations.cpython-312.pyc b/src/auto_commit_service/git/__pycache__/operations.cpython-312.pyc
index 64ab136..dd26ac0 100644
Binary files a/src/auto_commit_service/git/__pycache__/operations.cpython-312.pyc and b/src/auto_commit_service/git/__pycache__/operations.cpython-312.pyc differ
diff --git a/src/auto_commit_service/git/operations.py b/src/auto_commit_service/git/operations.py
index a94c09e..e5a0df4 100644
--- a/src/auto_commit_service/git/operations.py
+++ b/src/auto_commit_service/git/operations.py
@@ -166,7 +166,7 @@ async def git_add_all(repo_path: Path) -> None:
 
 
 async def git_check_ignored(repo_path: Path, files: list[str]) -> list[str]:
-    """Check which files are ignored by .gitignore.
+    """Check which files are ignored by .gitignore, including tracked files.
 
     Args:
         repo_path: Path to the repository
@@ -179,27 +179,55 @@ async def git_check_ignored(repo_path: Path, files: list[str]) -> list[str]:
         return []
 
     try:
-        # Use git check-ignore to filter out ignored files
-        # --stdin allows us to check multiple files efficiently
-        # -v flag would show matches, but we want non-matches
-        # Exit code 0 = files are ignored, 1 = files are NOT ignored
+        # CRITICAL: git check-ignore won't flag tracked files, even if now in .gitignore
+        # Use `ls-files -i --exclude-standard` to find tracked-but-ignored files
         file_list = "\n".join(files)
-        stdout, stderr, returncode = await _run_git_command(
+
+        # Check for tracked-but-ignored files (batch to avoid ARG_MAX)
+        tracked_ignored = set()
+        BATCH_SIZE = 1000
+        if len(files) > BATCH_SIZE:
+            for i in range(0, len(files), BATCH_SIZE):
+                batch = files[i : i + BATCH_SIZE]
+                stdout, _, _ = await _run_git_command(
+                    "ls-files", "-i", "--exclude-standard", "--",
+                    *batch,
+                    cwd=repo_path,
+                    check=False,
+                )
+                if stdout.strip():
+                    tracked_ignored.update(stdout.strip().split("\n"))
+        else:
+            tracked_ignored_stdout, _, _ = await _run_git_command(
+                "ls-files", "-i", "--exclude-standard", "--",
+                *files,
+                cwd=repo_path,
+                check=False,
+            )
+            if tracked_ignored_stdout.strip():
+                tracked_ignored = set(tracked_ignored_stdout.strip().split("\n"))
+
+        # Also check for untracked/new ignored files (uses stdin, no ARG_MAX issue)
+        untracked_ignored_stdout, _, _ = await _run_git_command(
             "check-ignore", "--stdin",
             cwd=repo_path,
             check=False,
             stdin=file_list.encode()
         )
+        untracked_ignored = set(untracked_ignored_stdout.strip().split("\n")) if untracked_ignored_stdout.strip() else set()
 
-        # Files in stdout are ignored - we want to exclude these
-        ignored_files = set(stdout.strip().split("\n")) if stdout.strip() else set()
+        # Combine both sets of ignored files
+        all_ignored = tracked_ignored | untracked_ignored
+
+        if all_ignored:
+            logger.info(f"Filtered {len(all_ignored)} gitignored files ({len(tracked_ignored)} tracked-but-ignored, {len(untracked_ignored)} new)")
 
         # Return only non-ignored files
-        return [f for f in files if f not in ignored_files]
+        return [f for f in files if f not in all_ignored]
 
-    except GitError:
-        # If check-ignore fails, return all files (safer than blocking commits)
-        logger.warning(f"git check-ignore failed in {repo_path}, proceeding without filter")
+    except GitError as e:
+        # If check fails, return all files (safer than blocking commits)
+        logger.warning(f"git ignore check failed in {repo_path}: {e}, proceeding without filter")
         return files