diff --git a/agent_builder/tools.py b/agent_builder/tools.py
index 03a4ea6..64d732e 100644
--- a/agent_builder/tools.py
+++ b/agent_builder/tools.py
@@ -213,6 +213,16 @@ def build_tools(ctx: ToolContext) -> list[Any]:
             return json.dumps({
                 "error": "no files in agents/" + name + "/ — write some first",
             })
+        try:
+            _assert_current_agent_project(bundle_bytes)
+        except RuntimeError as exc:
+            return json.dumps({
+                "error": str(exc),
+                "hint": (
+                    "Call init_agent_template first, then edit the generated "
+                    "DeepAgents files instead of replacing agent.py from memory."
+                ),
+            })
         b64 = base64.b64encode(bundle_bytes).decode("ascii")
         script = (
             "set -e\n"
@@ -279,6 +289,16 @@ def build_tools(ctx: ToolContext) -> list[Any]:
         bundle_bytes = _tarball_workspace_dir(s3, bucket, prefix)
         if not bundle_bytes:
             return json.dumps({"error": f"no files at agents/{name}/"})
+        try:
+            _assert_current_agent_project(bundle_bytes)
+        except RuntimeError as exc:
+            return json.dumps({
+                "error": str(exc),
+                "hint": (
+                    "Run init_agent_template again or restore the generated "
+                    "DeepAgents scaffold before deploying."
+                ),
+            })
 
         # Read the entrypoint from a2a.yaml so we can pass it verbatim.
         entrypoint = _read_entrypoint(bundle_bytes) or f"agent:{_class_name(name)}"
@@ -508,6 +528,32 @@ def _read_entrypoint(bundle: bytes) -> str | None:
     return None
 
 
+def _read_bundle_text(bundle: bytes, path: str) -> str | None:
+    try:
+        with tarfile.open(fileobj=io.BytesIO(bundle), mode="r:gz") as tf:
+            for member in tf.getmembers():
+                if member.name == path and member.isfile():
+                    extracted = tf.extractfile(member)
+                    if extracted is None:
+                        return None
+                    return extracted.read().decode("utf-8", "replace")
+    except Exception:  # noqa: BLE001
+        return None
+    return None
+
+
+def _assert_current_agent_project(bundle: bytes) -> None:
+    files = {
+        path: text
+        for path in ("agent.py", "requirements.txt")
+        if (text := _read_bundle_text(bundle, path)) is not None
+    }
+    _assert_current_deepagents_scaffold(
+        files,
+        source="agent project",
+    )
+
+
 def _class_name(slug: str) -> str:
     return "".join(p.capitalize() for p in re.split(r"[-_]+", slug) if p) or "MyAgent"
 
@@ -538,6 +584,17 @@ def _render_a2a_init_template(
 
 
 def _assert_current_a2a_init_template(files: dict[str, str]) -> None:
+    _assert_current_deepagents_scaffold(
+        files,
+        source="installed a2a-pack init template",
+    )
+
+
+def _assert_current_deepagents_scaffold(
+    files: dict[str, str],
+    *,
+    source: str,
+) -> None:
     required_markers = {
         "agent.py": (
             "LLMProvisioning.CALLER_PROVIDED",
@@ -567,7 +624,7 @@ def _assert_current_a2a_init_template(files: dict[str, str]) -> None:
     except Exception:  # noqa: BLE001
         version = "unknown"
     raise RuntimeError(
-        "installed a2a-pack init template is stale; expected the 0.1.3+ "
+        f"{source} is stale; expected the 0.1.3+ "
         "DeepAgents caller-LLM scaffold. "
         f"a2a_pack={version}; missing markers: {', '.join(missing)}"
     )
diff --git a/tests/test_template_init.py b/tests/test_template_init.py
index 7c901de..417cc9c 100644
--- a/tests/test_template_init.py
+++ b/tests/test_template_init.py
@@ -1,8 +1,11 @@
 from __future__ import annotations
 
+import io
+import tarfile
 import unittest
 
 from agent_builder.tools import (
+    _assert_current_agent_project,
     _assert_current_a2a_init_template,
     _render_a2a_init_template,
 )
@@ -35,3 +38,23 @@ class TemplateInitTests(unittest.TestCase):
                 "agent.py": "from a2a_pack import A2AAgent",
                 "requirements.txt": "httpx>=0.27",
             })
+
+    def test_stale_agent_project_is_rejected(self) -> None:
+        bundle = _tarball({
+            "agent.py": "from a2a_pack import A2AAgent\n",
+            "requirements.txt": "httpx>=0.27\n",
+        })
+
+        with self.assertRaisesRegex(RuntimeError, "agent project is stale"):
+            _assert_current_agent_project(bundle)
+
+
+def _tarball(files: dict[str, str]) -> bytes:
+    buf = io.BytesIO()
+    with tarfile.open(fileobj=buf, mode="w:gz") as tf:
+        for path, text in files.items():
+            body = text.encode("utf-8")
+            info = tarfile.TarInfo(path)
+            info.size = len(body)
+            tf.addfile(info, io.BytesIO(body))
+    return buf.getvalue()