diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b47caa41c76..a277442c6f9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2896,8 +2896,7 @@ demultiplexing step.")
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-flake8
-           python-poetry-core
+     (list python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm
index 31102eaa5b4..9b338792745 100644
--- a/gnu/packages/ebook.scm
+++ b/gnu/packages/ebook.scm
@@ -173,7 +173,6 @@ with Microsoft Compiled HTML (CHM) files.")
      (list bash-minimal
            cmake
            pkg-config
-           python-flake8
            python-pyqt-builder
            qtbase ; for qmake
            xdg-utils
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 1d166bf49d5..c3c21ef95cb 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1522,7 +1522,6 @@ learning.")
                ((",!=1.12\\.\\*") "")))))))
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-autograd
-                         python-flake8
                          python-flake8-bugbear
                          python-isort
                          python-matplotlib
@@ -6253,8 +6252,7 @@ and Numpy.")
     (build-system pyproject-build-system)
     (arguments '(#:tests? #false)) ;requires pyro
     (native-inputs
-     (list python-flake8
-           python-ipython
+     (list python-ipython
            python-pytest
            python-setuptools
            python-sphinx
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index f22bc7c6f3d..ef143270f7a 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4062,6 +4062,7 @@ formats, looking up tracks through metadata and audio fingerprints.")
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags '(list "--ignore=tests/quality/test_flake8.py")
        #:phases
        #~(modify-phases %standard-phases
            (add-before 'check 'remove-hypothesis-deadlines
@@ -4072,8 +4073,7 @@ formats, looking up tracks through metadata and audio fingerprints.")
                  (("( +)@given" all spaces)
                   (string-append spaces "@settings(deadline=None)\n" all))))))))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 79aac9a1a28..0a211759dd9 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3217,7 +3217,7 @@ origin than that of the web application.")
     (propagated-inputs
      (list python-orderedmultidict python-six))
     (native-inputs
-     (list python-flake8 python-pytest python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/gruns/furl")
     (synopsis "URL manipulation in Python")
     (description "Furl provides an easy-to-use alternative to the
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6e5846bc43e..18c0753258d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -31935,8 +31935,7 @@ Screenflick.")
     (propagated-inputs
      (list python-jinja2))
     (native-inputs
-     (list python-flake8
-           python-jinja2
+     (list python-jinja2
            python-pytest
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 729ba3516d3..fb4ddf6ac7f 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1506,7 +1506,6 @@ counters and tunnels).")
      (list pkg-config
            python-coverage
            python-decorator
-           python-flake8
            python-pkgconfig
            python-pytest
            python-setuptools
diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 3359a1e6656..3dc46777c3d 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -1241,7 +1241,6 @@ private network between hosts on the internet.")
     (native-inputs
      (list python-setuptools-scm
            ;; For tests only.
-           python-flake8
            python-mock
            python-poetry-core
            python-pytest-cov