diff --git a/apps/backend/init.py b/apps/backend/init.py
index 5f1962b4..19cfda82 100644
--- a/apps/backend/init.py
+++ b/apps/backend/init.py
@@ -4,8 +4,15 @@ Auto Claude project initialization utilities.
 Handles first-time setup of .auto-claude directory and ensures proper gitignore configuration.
 """
 
+import logging
+import os
+import subprocess
 from pathlib import Path
 
+from core.git_executable import get_git_executable
+
+logger = logging.getLogger(__name__)
+
 # All entries that should be added to .gitignore for auto-claude projects
 AUTO_CLAUDE_GITIGNORE_ENTRIES = [
     ".auto-claude/",
@@ -76,7 +83,83 @@ def ensure_gitignore_entry(project_dir: Path, entry: str = ".auto-claude/") -> b
         return True
 
 
-def ensure_all_gitignore_entries(project_dir: Path) -> list[str]:
+def _is_git_repo(project_dir: Path) -> bool:
+    """Check if the directory is a git repository."""
+    try:
+        result = subprocess.run(
+            [get_git_executable(), "rev-parse", "--is-inside-work-tree"],
+            cwd=project_dir,
+            capture_output=True,
+            text=True,
+            timeout=10,
+        )
+        return result.returncode == 0
+    except (subprocess.TimeoutExpired, Exception) as e:
+        logger.debug("Git repo check failed: %s", e)
+        return False
+
+
+def _commit_gitignore(project_dir: Path) -> bool:
+    """
+    Commit .gitignore changes with a standard message.
+
+    FIX (#1087): Auto-commit .gitignore changes to prevent merge failures.
+    Without this, merging tasks fails with "local changes would be overwritten".
+
+    Args:
+        project_dir: The project root directory
+
+    Returns:
+        True if commit succeeded, False otherwise
+    """
+    if not _is_git_repo(project_dir):
+        return False
+
+    try:
+        # Use LC_ALL=C to ensure English git output for reliable parsing
+        git_env = {**os.environ, "LC_ALL": "C"}
+
+        # Stage .gitignore
+        result = subprocess.run(
+            [get_git_executable(), "add", ".gitignore"],
+            cwd=project_dir,
+            capture_output=True,
+            text=True,
+            timeout=30,
+            env=git_env,
+        )
+        if result.returncode != 0:
+            return False
+
+        # Commit with standard message - explicitly specify .gitignore to avoid
+        # committing other staged files the user may have
+        result = subprocess.run(
+            [
+                get_git_executable(),
+                "commit",
+                ".gitignore",
+                "-m",
+                "chore: add auto-claude entries to .gitignore",
+            ],
+            cwd=project_dir,
+            capture_output=True,
+            text=True,
+            timeout=30,
+            env=git_env,
+        )
+        # Return True even if commit "fails" due to nothing to commit
+        # Check both stdout and stderr as message location varies by git version
+        combined_output = result.stdout + result.stderr
+        return result.returncode == 0 or "nothing to commit" in combined_output
+
+    except (subprocess.TimeoutExpired, Exception) as e:
+        logger.debug("Git commit failed: %s", e)
+        return False
+
+
+def ensure_all_gitignore_entries(
+    project_dir: Path, auto_commit: bool = False
+) -> list[str]:
     """
     Ensure all auto-claude related entries exist in the project's .gitignore file.
 
@@ -84,6 +167,7 @@ def ensure_all_gitignore_entries(project_dir: Path) -> list[str]:
 
     Args:
         project_dir: The project root directory
+        auto_commit: If True, automatically commit the .gitignore changes
 
     Returns:
         List of entries that were added (empty if all already existed)
@@ -120,6 +204,16 @@ def ensure_all_gitignore_entries(project_dir: Path) -> list[str]:
         added_entries.append(entry)
 
     gitignore_path.write_text(content)
+
+    # Auto-commit if requested and entries were added
+    if auto_commit and added_entries:
+        if not _commit_gitignore(project_dir):
+            logger.warning(
+                "Failed to auto-commit .gitignore changes in %s. "
+                "Manual commit may be required to avoid merge conflicts.",
+                project_dir,
+            )
+
     return added_entries
 
 
@@ -143,16 +237,17 @@ def init_auto_claude_dir(project_dir: Path) -> tuple[Path, bool]:
     auto_claude_dir.mkdir(parents=True, exist_ok=True)
 
     # Ensure all auto-claude entries are in .gitignore (only on first creation)
+    # FIX (#1087): Auto-commit the changes to prevent merge failures
     gitignore_updated = False
     if dir_created:
-        added = ensure_all_gitignore_entries(project_dir)
+        added = ensure_all_gitignore_entries(project_dir, auto_commit=True)
         gitignore_updated = len(added) > 0
     else:
         # Even if dir exists, check gitignore on first run
         # Use a marker file to track if we've already checked
         marker = auto_claude_dir / ".gitignore_checked"
         if not marker.exists():
-            added = ensure_all_gitignore_entries(project_dir)
+            added = ensure_all_gitignore_entries(project_dir, auto_commit=True)
             gitignore_updated = len(added) > 0
             marker.touch()
 
@@ -185,6 +280,7 @@ def repair_gitignore(project_dir: Path) -> list[str]:
     or when gitignore entries were manually removed.
 
     Also resets the .gitignore_checked marker to allow future updates.
+    Changes are automatically committed if the project is a git repository.
 
     Args:
         project_dir: The project root directory
@@ -200,8 +296,8 @@ def repair_gitignore(project_dir: Path) -> list[str]:
     if marker.exists():
         marker.unlink()
 
-    # Add all missing entries
-    added = ensure_all_gitignore_entries(project_dir)
+    # Add all missing entries and auto-commit
+    added = ensure_all_gitignore_entries(project_dir, auto_commit=True)
 
     # Re-create the marker
     if auto_claude_dir.exists():