diff --git a/utils.py b/utils.py
index 57bf0b19..09b319c3 100644
--- a/utils.py
+++ b/utils.py
@@ -198,6 +198,11 @@ def merge_toml(template, plugin_root_path, relative_path, template_vars):
             old_toml[merge_key] = data[merge_key]
         else:
             old_toml[merge_key].update(data[merge_key])
+        if template_vars["check_manifest"]:
+            check_manifest_conf = old_toml["tool"].setdefault("check-manifest", {"ignore": []})
+            for ai_file in ["AGENT.md", "CLAUDE.md"]:
+                if ai_file not in check_manifest_conf["ignore"]:
+                    check_manifest_conf["ignore"].append(ai_file)
         output = tomlkit.dumps(old_toml)
         if output[-1] != "\n":
             output = output + "\n"