diff --git a/code_review_graph/skills.py b/code_review_graph/skills.py
index 2ecc6d3..b94078a 100644
--- a/code_review_graph/skills.py
+++ b/code_review_graph/skills.py
@@ -382,11 +382,30 @@ def install_hooks(repo_root: Path) -> None:
     if settings_path.exists():
         try:
             existing = json.loads(settings_path.read_text())
+            backup_path = settings_dir / "settings.json.bak"
+            shutil.copy2(settings_path, backup_path)
+            logger.info("Backed up existing settings to %s", backup_path)
         except (json.JSONDecodeError, OSError) as exc:
             logger.warning("Could not read existing %s: %s", settings_path, exc)
 
     hooks_config = generate_hooks_config()
-    existing.update(hooks_config)
+    existing_hooks = existing.get("hooks", {})
+    if not isinstance(existing_hooks, dict):
+        logger.warning("Existing hooks config is not a dict; replacing with defaults")
+        existing_hooks = {}
+
+    merged_hooks = dict(existing_hooks)
+    for hook_name, hook_entries in hooks_config.get("hooks", {}).items():
+        if isinstance(merged_hooks.get(hook_name), list):
+            merged_list = list(merged_hooks[hook_name])
+            for entry in hook_entries:
+                if entry not in merged_list:
+                    merged_list.append(entry)
+            merged_hooks[hook_name] = merged_list
+        else:
+            merged_hooks[hook_name] = hook_entries
+
+    existing["hooks"] = merged_hooks
 
     settings_path.write_text(json.dumps(existing, indent=2) + "\n")
     logger.info("Wrote hooks config: %s", settings_path)
diff --git a/tests/test_skills.py b/tests/test_skills.py
index bad8b8b..d8d4e8e 100644
--- a/tests/test_skills.py
+++ b/tests/test_skills.py
@@ -130,10 +130,24 @@ def test_merges_with_existing(self, tmp_path):
 
         data = json.loads((settings_dir / "settings.json").read_text())
         assert data["customSetting"] is True
+        assert "OtherHook" in data["hooks"]
         assert "PostToolUse" in data["hooks"]
         assert "SessionStart" in data["hooks"]
         assert "PreCommit" in data["hooks"]
 
+    def test_creates_settings_backup(self, tmp_path):
+        settings_dir = tmp_path / ".claude"
+        settings_dir.mkdir(parents=True)
+        existing = {"hooks": {"OtherHook": []}}
+        (settings_dir / "settings.json").write_text(json.dumps(existing))
+
+        install_hooks(tmp_path)
+
+        backup_path = settings_dir / "settings.json.bak"
+        assert backup_path.exists()
+        backup = json.loads(backup_path.read_text())
+        assert backup == existing
+
     def test_creates_claude_directory(self, tmp_path):
         install_hooks(tmp_path)
         assert (tmp_path / ".claude").is_dir()