diff --git a/src/repoma/check_dev_files/__init__.py b/src/repoma/check_dev_files/__init__.py
index e560bdf7..529949ee 100644
--- a/src/repoma/check_dev_files/__init__.py
+++ b/src/repoma/check_dev_files/__init__.py
@@ -174,8 +174,8 @@ def main(argv: Optional[Sequence[str]] = None) -> int:
                 cron_frequency=args.pin_requirements,
             )
         executor(mypy.main)
-        executor(pytest.main)
         executor(pyright.main)
+        executor(pytest.main)
         executor(pyupgrade.main)
         executor(ruff.main)
         executor(setup_cfg.main, args.ignore_author)
diff --git a/src/repoma/check_dev_files/black.py b/src/repoma/check_dev_files/black.py
index bd05ccb9..fec49de3 100644
--- a/src/repoma/check_dev_files/black.py
+++ b/src/repoma/check_dev_files/black.py
@@ -6,8 +6,6 @@
 from repoma.utilities import CONFIG_PATH
 from repoma.utilities.executor import Executor
 from repoma.utilities.precommit import (
-    find_repo,
-    load_round_trip_precommit_config,
     update_precommit_hook,
     update_single_hook_precommit_repo,
 )
@@ -16,6 +14,7 @@
     get_sub_table,
     load_pyproject,
     to_toml_array,
+    update_nbqa_settings,
     write_pyproject,
 )
 from repoma.utilities.setup_cfg import get_supported_python_versions
@@ -27,9 +26,9 @@ def main() -> None:
     executor = Executor()
     executor(_remove_outdated_settings)
     executor(_update_black_settings)
-    executor(_update_nbqa_settings)
     executor(_update_precommit_repo)
     executor(_update_precommit_nbqa_hook)
+    executor(update_nbqa_settings, "black", to_toml_array(["--line-length=85"]))
     executor.finalize()
 
 
@@ -83,27 +82,3 @@ def _update_precommit_nbqa_hook() -> None:
             additional_dependencies=["black>=22.1.0"],
         ),
     )
-
-
-def _update_nbqa_settings() -> None:
-    # cspell:ignore addopts
-    if not CONFIG_PATH.precommit.exists():
-        return
-    if not __has_nbqa_precommit_repo():
-        return
-    pyproject = load_pyproject()
-    nbqa_table = get_sub_table(pyproject, "tool.nbqa.addopts", create=True)
-    expected = ["--line-length=85"]
-    if nbqa_table.get("black") != expected:
-        nbqa_table["black"] = expected
-        write_pyproject(pyproject)
-        msg = "Added nbQA configuration for black"
-        raise PrecommitError(msg)
-
-
-def __has_nbqa_precommit_repo() -> bool:
-    config, _ = load_round_trip_precommit_config()
-    nbqa_repo = find_repo(config, "https://github.com/nbQA-dev/nbQA")
-    if nbqa_repo is None:
-        return False
-    return True
diff --git a/src/repoma/check_dev_files/deprecated.py b/src/repoma/check_dev_files/deprecated.py
index fb9a4736..3146e406 100644
--- a/src/repoma/check_dev_files/deprecated.py
+++ b/src/repoma/check_dev_files/deprecated.py
@@ -1,6 +1,6 @@
 """Remove deprecated linters and formatters."""
 import os
-from typing import List
+from typing import TYPE_CHECKING, List
 
 from repoma.errors import PrecommitError
 from repoma.utilities import CONFIG_PATH
@@ -15,6 +15,9 @@
     set_setting,
 )
 
+if TYPE_CHECKING:
+    from tomlkit.items import Table
+
 
 def remove_deprecated_tools() -> None:
     executor = Executor()
@@ -28,6 +31,7 @@ def remove_deprecated_tools() -> None:
 def _remove_flake8() -> None:
     executor = Executor()
     executor(__remove_configs, [".flake8"])
+    executor(__remove_nbqa_option, "flake8")
     executor(__uninstall, "flake8", check_options=["lint", "sty"])
     executor(__uninstall, "pep8-naming", check_options=["lint", "sty"])
     executor(remove_extension_recommendation, "ms-python.flake8", unwanted=True)
@@ -42,6 +46,7 @@ def _remove_flake8() -> None:
 def _remove_isort() -> None:
     executor = Executor()
     executor(__remove_isort_settings)
+    executor(__remove_nbqa_option, "isort")
     executor(remove_extension_recommendation, "ms-python.isort", unwanted=True)
     executor(remove_precommit_hook, "isort")
     executor(remove_precommit_hook, "nbqa-isort")
@@ -50,6 +55,30 @@ def _remove_isort() -> None:
     executor.finalize()
 
 
+def __remove_isort_settings() -> None:
+    pyproject = load_pyproject()
+    if pyproject.get("tool", {}).get("isort") is None:
+        return
+    pyproject["tool"].remove("isort")  # type: ignore[union-attr]
+    write_pyproject(pyproject)
+    msg = f"Removed [tool.isort] section from {CONFIG_PATH.pyproject}"
+    raise PrecommitError(msg)
+
+
+def __remove_nbqa_option(option: str) -> None:
+    pyproject = load_pyproject()
+    # cspell:ignore addopts
+    nbqa_table: Table = pyproject.get("tool", {}).get("nbqa", {}).get("addopts")
+    if nbqa_table is None:
+        return
+    if nbqa_table.get(option) is None:
+        return
+    nbqa_table.remove(option)
+    write_pyproject(pyproject)
+    msg = f"Removed {option!r} nbQA options from {CONFIG_PATH.pyproject}"
+    raise PrecommitError(msg)
+
+
 def _remove_pydocstyle() -> None:
     executor = Executor()
     executor(
@@ -77,16 +106,6 @@ def _remove_pylint() -> None:
     executor.finalize()
 
 
-def __remove_isort_settings() -> None:
-    pyproject = load_pyproject()
-    if pyproject.get("tool", {}).get("isort") is None:
-        return
-    pyproject["tool"].remove("isort")  # type: ignore[union-attr]
-    write_pyproject(pyproject)
-    msg = f"Removed [tool.isort] section from {CONFIG_PATH.pyproject}"
-    raise PrecommitError(msg)
-
-
 def __remove_configs(paths: List[str]) -> None:
     executor = Executor()
     for path in paths:
diff --git a/src/repoma/check_dev_files/ruff.py b/src/repoma/check_dev_files/ruff.py
index 4758fd89..af3c200a 100644
--- a/src/repoma/check_dev_files/ruff.py
+++ b/src/repoma/check_dev_files/ruff.py
@@ -20,6 +20,7 @@
     get_sub_table,
     load_pyproject,
     to_toml_array,
+    update_nbqa_settings,
     write_pyproject,
 )
 from repoma.utilities.readme import add_badge
@@ -40,6 +41,7 @@ def main() -> None:
     executor(_update_precommit_hook)
     executor(_update_precommit_nbqa_hook)
     executor(_update_vscode_settings)
+    executor(update_nbqa_settings, "ruff", to_toml_array(["--line-length=85"]))
     executor.finalize()
 
 
diff --git a/src/repoma/utilities/pyproject.py b/src/repoma/utilities/pyproject.py
index 99db8510..2f02e5c9 100644
--- a/src/repoma/utilities/pyproject.py
+++ b/src/repoma/utilities/pyproject.py
@@ -7,7 +7,9 @@
 from tomlkit.items import Array, Table
 from tomlkit.toml_document import TOMLDocument
 
+from repoma.errors import PrecommitError
 from repoma.utilities import CONFIG_PATH
+from repoma.utilities.precommit import find_repo, load_round_trip_precommit_config
 
 
 def complies_with_subset(settings: dict, minimal_settings: dict) -> bool:
@@ -48,4 +50,29 @@ def to_toml_array(items: Iterable[Any]) -> Array:
     array.extend(items)
     if len(array) > 1:
         array.multiline(True)
+    else:
+        array.multiline(False)
     return array
+
+
+def update_nbqa_settings(key: str, expected: Any) -> None:
+    # cspell:ignore addopts
+    if not CONFIG_PATH.precommit.exists():
+        return
+    if not __has_nbqa_precommit_repo():
+        return
+    pyproject = load_pyproject()
+    nbqa_table = get_sub_table(pyproject, "tool.nbqa.addopts", create=True)
+    if nbqa_table.get(key) != expected:
+        nbqa_table[key] = expected
+        write_pyproject(pyproject)
+        msg = f"Added nbQA configuration for {key!r}"
+        raise PrecommitError(msg)
+
+
+def __has_nbqa_precommit_repo() -> bool:
+    config, _ = load_round_trip_precommit_config()
+    nbqa_repo = find_repo(config, "https://github.com/nbQA-dev/nbQA")
+    if nbqa_repo is None:
+        return False
+    return True