diff --git a/pkgs/by-name/fl/flye/package.nix b/pkgs/by-name/fl/flye/package.nix
index 76ea84a1c9a0..0efcde87220e 100644
--- a/pkgs/by-name/fl/flye/package.nix
+++ b/pkgs/by-name/fl/flye/package.nix
@@ -1,5 +1,6 @@
 { lib
 , fetchFromGitHub
+, fetchpatch
 , python3Packages
 , zlib
 , curl
@@ -29,15 +30,29 @@ python3Packages.buildPythonApplication rec {
     libdeflate
   ];
 
-  patches = [ ./aarch64-fix.patch ];
+  patches = [
+    ./aarch64-fix.patch
+    (fetchpatch {
+      # https://github.com/mikolmogorov/Flye/pull/711
+      name = "remove-distutils.patch";
+      url = "https://github.com/mikolmogorov/Flye/commit/fb34f1ccfdf569d186a4ce822ee18eced736636b.patch";
+      hash = "sha256-52bnZ8XyP0HsY2OpNYMU3xJgotNVdQc/O2w3XIReUdQ=";
+    })
+    (fetchpatch {
+      # https://github.com/mikolmogorov/Flye/pull/670
+      name = "remove-find_module.patch";
+      url = "https://github.com/mikolmogorov/Flye/commit/441b1c6eb0f60b7c4fb1a40d659c7dabb7ad41b6.patch";
+      hash = "sha256-RytFIN1STK33/nvXpck6woQcwV/e1fmA8AgmptiIiDU=";
+    })
+  ];
 
   postPatch = ''
     substituteInPlace flye/polishing/alignment.py \
       --replace-fail "/bin/bash" "${lib.getExe bash}"
+  '';
 
-    substituteInPlace flye/tests/test_toy.py \
-      --replace-fail "find_executable(\"flye" "find_executable(\"$out/bin/flye" \
-      --replace-fail "[\"flye" "[\"$out/bin/flye"
+  preCheck = ''
+    export PATH=$out/bin:$PATH
   '';
 
   meta = with lib; {