diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9df95648774..26bf4803ef6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,13 +5,14 @@ repos:
     rev: 4.3.21-2
     hooks:
       - id: isort
+        files: .+\.py$
   # https://github.com/python/black#version-control-integration
   - repo: https://github.com/python/black
     rev: stable
     hooks:
       - id: black
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.2.3
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.9
     hooks:
       - id: flake8
   - repo: https://github.com/pre-commit/mirrors-mypy
diff --git a/doc/whats-new.rst b/doc/whats-new.rst
index bd0851d2b39..39aaa0e4fd3 100644
--- a/doc/whats-new.rst
+++ b/doc/whats-new.rst
@@ -54,6 +54,9 @@ Documentation
 
 Internal Changes
 ~~~~~~~~~~~~~~~~
+- Run the ``isort`` pre-commit hook only on python source files
+  and update the ``flake8`` version. (:issue:`3750`, :pull:`3711`)
+  By `Justus Magin <https://github.com/keewis>`_.
 
 
 .. _whats-new.0.15.1: