diff --git a/src/deepscientist/runners/codex.py b/src/deepscientist/runners/codex.py
index ff9c9d5d..0e3e7aed 100644
--- a/src/deepscientist/runners/codex.py
+++ b/src/deepscientist/runners/codex.py
@@ -2,6 +2,7 @@
 
 import json
 import os
+import re
 import signal
 import subprocess
 import sys
@@ -95,6 +96,8 @@
         "bash_exec",
     ),
 }
+_BUILTIN_MCP_SERVER_NAMES = tuple(_BUILTIN_MCP_TOOL_APPROVALS)
+_TOML_TABLE_HEADER_PATTERN = re.compile(r"^\s*(\[\[?)\s*([^\]]+?)\s*(\]\]?)\s*(?:#.*)?$")
 
 
 def _builtin_mcp_tool_approvals_for_profile(custom_profile: str | None) -> dict[str, tuple[str, ...]]:
@@ -111,6 +114,34 @@ def _builtin_mcp_tool_approvals_for_profile(custom_profile: str | None) -> dict[
         }
     return _BUILTIN_MCP_TOOL_APPROVALS
 
+
+def _strip_builtin_mcp_server_sections(
+    config_text: str,
+    server_names: tuple[str, ...] = _BUILTIN_MCP_SERVER_NAMES,
+) -> str:
+    if not str(config_text or "").strip() or not server_names:
+        return str(config_text or "").rstrip()
+
+    server_prefixes = tuple(
+        prefix
+        for name in server_names
+        for prefix in (
+            f"mcp_servers.{name}",
+            f'mcp_servers."{name}"',
+            f"mcp_servers.'{name}'",
+        )
+    )
+    filtered_lines: list[str] = []
+    skipping = False
+    for line in str(config_text or "").splitlines():
+        match = _TOML_TABLE_HEADER_PATTERN.match(line)
+        if match is not None:
+            header = re.sub(r"\s+", "", match.group(2))
+            skipping = any(header == prefix or header.startswith(f"{prefix}.") for prefix in server_prefixes)
+        if not skipping:
+            filtered_lines.append(line)
+    return "\n".join(filtered_lines).rstrip()
+
 _PROVIDER_ENV_CONFLICT_KEYS = (
     "OPENAI_API_KEY",
     "OPENAI_BASE_URL",
@@ -1544,6 +1575,7 @@ def _inject_built_in_mcp(
             prefix = existing.split(marker_start, 1)[0].rstrip()
         else:
             prefix = existing.rstrip()
+        prefix = _strip_builtin_mcp_server_sections(prefix)
 
         pythonpath = os.environ.get("PYTHONPATH", "")
         resolved_runner_config = runner_config if isinstance(runner_config, dict) else self._load_runner_config()
diff --git a/tests/test_codex_runner.py b/tests/test_codex_runner.py
index 4be5bd52..cc795bee 100644
--- a/tests/test_codex_runner.py
+++ b/tests/test_codex_runner.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import json
+import tomllib
 from pathlib import Path
 from types import SimpleNamespace
 
@@ -695,6 +696,84 @@ def test_codex_runner_injects_builtin_mcp_tool_approval_overrides(temp_home) ->
     assert config_text.count('approval_mode = "approve"') >= 3
 
 
+def test_codex_runner_replaces_copied_builtin_mcp_sections_before_injection(temp_home) -> None:  # type: ignore[no-untyped-def]
+    source_codex_home = temp_home / "source-codex-home"
+    source_codex_home.mkdir(parents=True, exist_ok=True)
+    (source_codex_home / "config.toml").write_text(
+        "\n".join(
+            [
+                'model_provider = "ananapi"',
+                "",
+                "[mcp_servers.memory]",
+                'transport = "stdio"',
+                'command = "old-memory-server"',
+                "",
+                "[mcp_servers.memory.env]",
+                'OLD_MEMORY = "1"',
+                "",
+                "[mcp_servers.memory.tools.list_recent]",
+                'approval_mode = "never"',
+                "",
+                "[mcp_servers.artifact]",
+                'transport = "stdio"',
+                'command = "old-artifact-server"',
+                "",
+                "[mcp_servers.bash_exec]",
+                'transport = "stdio"',
+                'command = "old-bash-server"',
+                "",
+                "[mcp_servers.bash_exec.env]",
+                'OLD_BASH = "1"',
+                "",
+                "[mcp_servers.custom]",
+                'transport = "stdio"',
+                'command = "custom-server"',
+                "",
+                "[mcp_servers.custom.env]",
+                'CUSTOM = "1"',
+            ]
+        )
+        + "\n",
+        encoding="utf-8",
+    )
+    (source_codex_home / "auth.json").write_text("{}\n", encoding="utf-8")
+
+    quest_root = temp_home / "quest"
+    quest_root.mkdir(parents=True, exist_ok=True)
+    workspace_root = quest_root
+
+    runner = CodexRunner(
+        home=temp_home,
+        repo_root=temp_home,
+        binary="codex",
+        logger=object(),  # type: ignore[arg-type]
+        prompt_builder=object(),  # type: ignore[arg-type]
+        artifact_service=object(),  # type: ignore[arg-type]
+    )
+
+    codex_home = runner._prepare_project_codex_home(
+        workspace_root,
+        quest_root=quest_root,
+        quest_id="q-001",
+        run_id="run-001",
+        runner_config={"config_dir": str(source_codex_home)},
+    )
+
+    config_text = (codex_home / "config.toml").read_text(encoding="utf-8")
+    parsed = tomllib.loads(config_text)
+    assert config_text.count("[mcp_servers.memory]") == 1
+    assert config_text.count("[mcp_servers.artifact]") == 1
+    assert config_text.count("[mcp_servers.bash_exec]") == 1
+    assert "old-memory-server" not in config_text
+    assert "old-artifact-server" not in config_text
+    assert "old-bash-server" not in config_text
+    assert "OLD_MEMORY" not in config_text
+    assert "OLD_BASH" not in config_text
+    assert parsed["mcp_servers"]["memory"]["transport"] == "stdio"
+    assert parsed["mcp_servers"]["custom"]["command"] == "custom-server"
+    assert parsed["mcp_servers"]["custom"]["env"]["CUSTOM"] == "1"
+
+
 def test_codex_runner_restricts_settings_issue_profile_to_issue_tool_and_bash_exec_only(temp_home) -> None:  # type: ignore[no-untyped-def]
     source_codex_home = temp_home / "source-codex-home"
     source_codex_home.mkdir(parents=True, exist_ok=True)