diff --git a/.markdownlint.json b/.markdownlint.json
deleted file mode 100644
index 23bb7fa6..00000000
--- a/.markdownlint.json
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-  "MD013": { "line_length": 88 },
-  "MD026": { "punctuation": ".,;:。，；：！" },
-  "MD033": {
-    "allowed_elements": ["br"]
-  }
-}
diff --git a/src/repoma/check_dev_files/deprecated.py b/src/repoma/check_dev_files/deprecated.py
index 3c5d972c..de89c2a3 100644
--- a/src/repoma/check_dev_files/deprecated.py
+++ b/src/repoma/check_dev_files/deprecated.py
@@ -25,6 +25,7 @@ def remove_deprecated_tools(keep_issue_templates: bool) -> None:
     executor(_remove_isort)
     if not keep_issue_templates:
         executor(_remove_github_issue_templates)
+    executor(_remove_markdownlint)
     executor(_remove_pydocstyle)
     executor(_remove_pylint)
     executor.finalize()
@@ -39,7 +40,6 @@ 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()
@@ -50,12 +50,6 @@ 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")
@@ -97,6 +91,20 @@ def _remove_github_issue_templates() -> None:
     )
 
 
+def _remove_markdownlint() -> None:
+    executor = Executor()
+    executor(__remove_configs, [".markdownlint.json", ".markdownlint.yaml"])
+    executor(__remove_from_gitignore, ".markdownlint.json")
+    executor(
+        remove_extension_recommendation,
+        # cspell:ignore davidanson markdownlint
+        extension_name="davidanson.vscode-markdownlint",
+        unwanted=True,
+    )
+    executor(remove_precommit_hook, "markdownlint")
+    executor.finalize()
+
+
 def _remove_pydocstyle() -> None:
     executor = Executor()
     executor(
@@ -115,7 +123,6 @@ 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")