diff --git a/graphify/__main__.py b/graphify/__main__.py
index 604fa5248..df53c8bea 100644
--- a/graphify/__main__.py
+++ b/graphify/__main__.py
@@ -217,10 +217,13 @@ def _install_gemini_hook(project_dir: Path) -> None:
     except json.JSONDecodeError:
         settings = {}
     before_tool = settings.setdefault("hooks", {}).setdefault("BeforeTool", [])
-    if any("graphify" in str(h) for h in before_tool):
-        print("  .gemini/settings.json  ->  hook already registered (no change)")
-        return
-    before_tool.append(_GEMINI_HOOK)
+
+    # Remove any existing graphify hooks (handles upgrades from old versions)
+    filtered = [h for h in before_tool if "graphify" not in str(h)]
+    settings["hooks"]["BeforeTool"] = filtered
+
+    # Install fresh hook
+    settings["hooks"]["BeforeTool"].append(_GEMINI_HOOK)
     settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
     print("  .gemini/settings.json  ->  BeforeTool hook registered")
 
@@ -417,11 +420,13 @@ def _install_codex_hook(project_dir: Path) -> None:
         existing = {}
 
     pre_tool = existing.setdefault("hooks", {}).setdefault("PreToolUse", [])
-    if any("graphify" in str(h) for h in pre_tool):
-        print(f"  .codex/hooks.json  ->  hook already registered (no change)")
-        return
 
-    pre_tool.extend(_CODEX_HOOK["hooks"]["PreToolUse"])
+    # Remove any existing graphify hooks (handles upgrades from old versions)
+    filtered = [h for h in pre_tool if "graphify" not in str(h)]
+    existing["hooks"]["PreToolUse"] = filtered
+
+    # Install fresh hook with correct format
+    existing["hooks"]["PreToolUse"].extend(_CODEX_HOOK["hooks"]["PreToolUse"])
     hooks_path.write_text(json.dumps(existing, indent=2), encoding="utf-8")
     print(f"  .codex/hooks.json  ->  PreToolUse hook registered")
 
@@ -540,12 +545,12 @@ def _install_claude_hook(project_dir: Path) -> None:
     hooks = settings.setdefault("hooks", {})
     pre_tool = hooks.setdefault("PreToolUse", [])
 
-    # Check if already installed
-    if any(h.get("matcher") == "Glob|Grep" and "graphify" in str(h) for h in pre_tool):
-        print(f"  .claude/settings.json  ->  hook already registered (no change)")
-        return
+    # Remove any existing graphify hooks (handles upgrades from old versions)
+    filtered = [h for h in pre_tool if not (h.get("matcher") == "Glob|Grep" and "graphify" in str(h))]
+    settings["hooks"]["PreToolUse"] = filtered
 
-    pre_tool.append(_SETTINGS_HOOK)
+    # Install fresh hook
+    settings["hooks"]["PreToolUse"].append(_SETTINGS_HOOK)
     settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
     print(f"  .claude/settings.json  ->  PreToolUse hook registered")