diff --git a/scripts-dev/lint.sh b/scripts-dev/lint.sh
index 6f1ba22931..66b0568858 100755
--- a/scripts-dev/lint.sh
+++ b/scripts-dev/lint.sh
@@ -15,7 +15,7 @@ else
 fi
 
 echo "Linting these locations: $files"
-isort -y -rc $files
+isort $files
 python3 -m black $files
 ./scripts-dev/config-lint.sh
 flake8 $files
diff --git a/setup.cfg b/setup.cfg
index f2bca272e1..a32278ea8a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -26,7 +26,6 @@ ignore=W503,W504,E203,E731,E501
 
 [isort]
 line_length = 88
-not_skip = __init__.py
 sections=FUTURE,STDLIB,COMPAT,THIRDPARTY,TWISTED,FIRSTPARTY,TESTS,LOCALFOLDER
 default_section=THIRDPARTY
 known_first_party = synapse