diff --git a/.flake8 b/.flake8
deleted file mode 100644
index 209066837b..0000000000
--- a/.flake8
+++ /dev/null
@@ -1,10 +0,0 @@
-[flake8]
-max-line-length = 99
-doctests = False
-exclude=*build/
-ignore =
-    E203
-    W503
-per-file-ignores =
-    **/__init__.py : F401
-    docs/conf.py : E265
diff --git a/pyproject.toml b/pyproject.toml
index 9b9a0c1b01..bb8aea305f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -99,22 +99,9 @@ version-file = "src/smriprep/_version.py"
 # Developer tool configurations
 #
 
+# Disable black
 [tool.black]
-line-length = 99
-skip-string-normalization = true
-
-[tool.isort]
-profile = 'black'
-
-[tool.flake8]
-max-line-length = "99"
-doctests = "False"
-exclude = "*build/"
-ignore = ["W503", "E203"]
-per-file-ignores = [
-    "**/__init__.py : F401",
-    "docs/conf.py : E265",
-]
+exclude = ".*"
 
 [tool.pytest.ini_options]
 minversion = "8"
diff --git a/wrapper/setup.cfg b/wrapper/setup.cfg
index 65a188cd05..072a379d3a 100644
--- a/wrapper/setup.cfg
+++ b/wrapper/setup.cfg
@@ -24,6 +24,3 @@ console_scripts =
 
 [bdist_wheel]
 universal=1
-
-[flake8]
-max-line-length = 99