diff --git a/pkgs/development/python-modules/onnx/default.nix b/pkgs/development/python-modules/onnx/default.nix
index ce9d31be5aa0..0af451607af3 100644
--- a/pkgs/development/python-modules/onnx/default.nix
+++ b/pkgs/development/python-modules/onnx/default.nix
@@ -8,9 +8,6 @@
   pybind11,
   setuptools,
 
-  # nativeBuildInputs
-  protobuf-core,
-
   # buildInputs
   abseil-cpp,
   protobuf,
@@ -48,10 +45,6 @@ buildPythonPackage rec {
     setuptools
   ];
 
-  nativeBuildInputs = [
-    protobuf-core # `protoc` required
-  ];
-
   buildInputs = [
     abseil-cpp
     gtestStatic
diff --git a/pkgs/development/python-modules/onnxconverter-common/default.nix b/pkgs/development/python-modules/onnxconverter-common/default.nix
index 94cc0b881351..87d83797fbfd 100644
--- a/pkgs/development/python-modules/onnxconverter-common/default.nix
+++ b/pkgs/development/python-modules/onnxconverter-common/default.nix
@@ -2,6 +2,7 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+  setuptools,
   numpy,
   packaging,
   protobuf,
@@ -14,7 +15,7 @@ buildPythonPackage rec {
   pname = "onnxconverter-common";
   version = "1.14.0";
 
-  format = "setuptools";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "microsoft";
@@ -23,7 +24,13 @@ buildPythonPackage rec {
     hash = "sha256-NbHyjLcr/Gq1zRiJW3ZBpEVQGVQGhp7SmfVd5hBIi2o=";
   };
 
-  propagatedBuildInputs = [
+  build-system = [
+    setuptools
+  ];
+
+  pythonRelaxDeps = [ "protobuf" ];
+
+  dependencies = [
     numpy
     packaging
     protobuf
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 2b91ac96acde..48bdda41d3ca 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -9340,13 +9340,9 @@ self: super: with self; {
 
   onlykey-solo-python = callPackage ../development/python-modules/onlykey-solo-python { };
 
-  onnx = callPackage ../development/python-modules/onnx {
-    protobuf-core = pkgs.protobuf;
-  };
+  onnx = callPackage ../development/python-modules/onnx { };
 
-  onnxconverter-common = callPackage ../development/python-modules/onnxconverter-common {
-    inherit (pkgs) protobuf;
-  };
+  onnxconverter-common = callPackage ../development/python-modules/onnxconverter-common { };
 
   onnxmltools = callPackage ../development/python-modules/onnxmltools { };