diff --git a/.gitignore b/.gitignore
index 2cac2bc6..fb10abe8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -45,7 +45,6 @@ pyvenv*/
 !.github/*.yml
 !.github/*/*.yml
 !.gitpod.yml
-!.markdownlint.json
 !.pre-commit-config.yaml
 !.pre-commit-hooks.yaml
 !.readthedocs.yml
diff --git a/.gitpod.yml b/.gitpod.yml
index 2f71116c..f92255f1 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -15,7 +15,6 @@ vscode:
   extensions:
     - charliermarsh.ruff
     - christian-kohler.path-intellisense
-    - davidanson.vscode-markdownlint
     - eamodio.gitlens
     - editorconfig.editorconfig
     - esbenp.prettier-vscode
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 18ef9e36..2958c902 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -87,11 +87,6 @@ repos:
             .*\.py
           )$
 
-  - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.35.0
-    hooks:
-      - id: markdownlint
-
   - repo: local
     hooks:
       - id: mypy
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
index 6a5b9641..0ec4f1f6 100644
--- a/.vscode/extensions.json
+++ b/.vscode/extensions.json
@@ -2,7 +2,6 @@
   "recommendations": [
     "charliermarsh.ruff",
     "christian-kohler.path-intellisense",
-    "davidanson.vscode-markdownlint",
     "eamodio.gitlens",
     "editorconfig.editorconfig",
     "esbenp.prettier-vscode",
@@ -24,6 +23,7 @@
   ],
   "unwantedRecommendations": [
     "bungcip.better-toml",
+    "davidanson.vscode-markdownlint",
     "ms-python.flake8",
     "ms-python.isort",
     "ms-python.pylint",
diff --git a/src/repoma/check_dev_files/deprecated.py b/src/repoma/check_dev_files/deprecated.py
index f36dac3c..9df1f047 100644
--- a/src/repoma/check_dev_files/deprecated.py
+++ b/src/repoma/check_dev_files/deprecated.py
@@ -36,6 +36,7 @@ def _remove_flake8() -> None:
     executor(remove_extension_recommendation, "ms-python.flake8", unwanted=True)
     executor(remove_precommit_hook, "autoflake")  # cspell:ignore autoflake
     executor(remove_precommit_hook, "flake8")
+    executor(remove_precommit_hook, "markdownlint")
     executor(remove_precommit_hook, "nbqa-flake8")
     executor(remove_settings, ["flake8.importStrategy"])
     executor.finalize()
@@ -46,6 +47,12 @@ def _remove_isort() -> None:
     executor(__remove_isort_settings)
     executor(__remove_nbqa_option, "black")
     executor(__remove_nbqa_option, "isort")
+    executor(
+        remove_extension_recommendation,
+        # cspell:ignore davidanson markdownlint
+        extension_name="davidanson.vscode-markdownlint",
+        unwanted=True,
+    )
     executor(remove_extension_recommendation, "ms-python.isort", unwanted=True)
     executor(remove_precommit_hook, "isort")
     executor(remove_precommit_hook, "nbqa-isort")
@@ -96,6 +103,7 @@ def _remove_pydocstyle() -> None:
 def _remove_pylint() -> None:
     executor = Executor()
     executor(__remove_configs, [".pylintrc"])  # cspell:ignore pylintrc
+    executor(__remove_from_gitignore, ".markdownlint.json")
     executor(__uninstall, "pylint", check_options=["lint", "sty"])
     executor(remove_extension_recommendation, "ms-python.pylint", unwanted=True)
     executor(remove_precommit_hook, "pylint")
@@ -133,3 +141,18 @@ def __uninstall(package: str, check_options: List[str]) -> None:
             continue
         msg = f'Please remove {package} from the "{section}" section of setup.cfg'
         raise PrecommitError(msg)
+
+
+def __remove_from_gitignore(pattern: str) -> None:
+    gitignore_path = ".gitignore"
+    if not os.path.exists(gitignore_path):
+        return
+    with open(gitignore_path) as f:
+        lines = f.readlines()
+    filtered_lines = [s for s in lines if pattern not in s]
+    if filtered_lines == lines:
+        return
+    with open(gitignore_path, "w") as f:
+        f.writelines(filtered_lines)
+    msg = f"Removed {pattern} from {gitignore_path}"
+    raise PrecommitError(msg)