diff --git a/pkgs/development/python-modules/cypari2/default.nix b/pkgs/development/python-modules/cypari2/default.nix
index 5b5ca31e4d02..5a1096cb1505 100644
--- a/pkgs/development/python-modules/cypari2/default.nix
+++ b/pkgs/development/python-modules/cypari2/default.nix
@@ -30,20 +30,13 @@ buildPythonPackage rec {
     })
   ];
 
-  # This differs slightly from the default python installPhase in that it pip-installs
-  # "." instead of "*.whl".
-  # That is because while the default install phase succeeds to build the package,
-  # it fails to generate the file "auto_paridecl.pxd".
-  installPhase = ''
-    export PYTHONPATH="$out/${python.sitePackages}:$PYTHONPATH"
-
-    # install "." instead of "*.whl"
-    pip install . --no-index --no-warn-script-location --prefix="$out" --no-cache
+  preBuild = ''
+    # generate cythonized extensions (auto_paridecl.pxd is crucial)
+    ${python.pythonOnBuildForHost.interpreter} setup.py build_ext --inplace
   '';
 
   nativeBuildInputs = [
     pari
-    python.pythonOnBuildForHost.pkgs.pip
   ];
 
   buildInputs = [
@@ -56,6 +49,7 @@ buildPythonPackage rec {
   ];
 
   checkPhase = ''
+    test -f "$out/${python.sitePackages}/cypari2/auto_paridecl.pxd"
     make check
   '';
 
diff --git a/pkgs/development/python-modules/cysignals/default.nix b/pkgs/development/python-modules/cysignals/default.nix
index fe0ca2e17a09..b64d3f8d7174 100644
--- a/pkgs/development/python-modules/cysignals/default.nix
+++ b/pkgs/development/python-modules/cysignals/default.nix
@@ -1,8 +1,9 @@
 { lib
 , autoreconfHook
+, fetchpatch
 , fetchPypi
 , buildPythonPackage
-, cython_3
+, cython
 , pariSupport ? true, pari # for interfacing with the PARI/GP signal handler
 }:
 
@@ -18,6 +19,14 @@ buildPythonPackage rec {
     hash = "sha256-Dx4yHlWgf5AchqNqHkSX9v+d/nAGgdATCjjDbk6yOMM=";
   };
 
+  patches = [
+    # https://github.com/sagemath/cysignals/pull/193
+    (fetchpatch {
+      url = "https://github.com/sagemath/cysignals/commit/474179c87ab0ff562fdfd2471b02797e4bdd3148.diff";
+      sha256 = "sha256-qEAmf4kU+QDI/JPFNjQMZIjMBk8dnaLmOpagIBMsh7w=";
+    })
+  ];
+
   # explicit check:
   # build/src/cysignals/implementation.c:27:2: error: #error "cysignals must be compiled without _FORTIFY_SOURCE"
   hardeningDisable = [
@@ -34,7 +43,7 @@ buildPythonPackage rec {
   '';
 
   propagatedBuildInputs = [
-    cython_3
+    cython
   ] ++ lib.optionals pariSupport [
     # When cysignals is built with pari, including cysignals into the
     # buildInputs of another python package will cause cython to link against
diff --git a/pkgs/development/python-modules/fpylll/default.nix b/pkgs/development/python-modules/fpylll/default.nix
index 2de77cfbd69d..be738b90e198 100644
--- a/pkgs/development/python-modules/fpylll/default.nix
+++ b/pkgs/development/python-modules/fpylll/default.nix
@@ -1,10 +1,11 @@
 { lib
 , fetchFromGitHub
+, fetchpatch
 , buildPythonPackage
 
 # build-system
 , cysignals
-, cython_3
+, cython
 , pkgconfig
 , setuptools
 
@@ -30,8 +31,21 @@ buildPythonPackage rec {
     hash = "sha256-EyReCkVRb3CgzIRal5H13OX/UdwWi+evDe7PoS1qP4A=";
   };
 
+  # temporarily revert to cython 0.29
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/fplll/fpylll/commit/528243c6fa6491c8e9652b99bdf9758766273d66.diff";
+      revert = true;
+      sha256 = "sha256-IRppkESy0CRwARhxBAsZxP6JkTe0M91apG4CTSSYNUU=";
+      excludes = ["requirements.txt"];
+    })
+  ];
+  postPatch = ''
+    substituteInPlace requirements.txt --replace "Cython>=3.0" "Cython"
+  '';
+
   nativeBuildInputs = [
-    cython_3
+    cython
     cysignals
     pkgconfig
     setuptools