diff --git a/pkgs/by-name/on/onnxruntime/package.nix b/pkgs/by-name/on/onnxruntime/package.nix
index 0ba0c138a825..dbe82a0e2edc 100644
--- a/pkgs/by-name/on/onnxruntime/package.nix
+++ b/pkgs/by-name/on/onnxruntime/package.nix
@@ -4,6 +4,7 @@
   stdenv,
   fetchFromGitHub,
   abseil-cpp_202508,
+  buildPackages,
   cmake,
   cpuinfo,
   eigen,
@@ -163,7 +164,6 @@ effectiveStdenv.mkDerivation (finalAttrs: {
     cmake
     pkg-config
     python3Packages.python
-    protobuf
   ]
   ++ lib.optionals pythonSupport (
     with python3Packages;
@@ -240,10 +240,7 @@ effectiveStdenv.mkDerivation (finalAttrs: {
     (darwinMinVersionHook "13.3")
   ];
 
-  nativeCheckInputs = [
-    gtest
-  ]
-  ++ lib.optionals pythonSupport (
+  nativeCheckInputs = lib.optionals pythonSupport (
     with python3Packages;
     [
       onnx
@@ -252,6 +249,10 @@ effectiveStdenv.mkDerivation (finalAttrs: {
     ]
   );
 
+  checkInputs = [
+    gtest
+  ];
+
   # TODO: build server, and move .so's to lib output
   # Python's wheel is stored in a separate dist output
   outputs = [
@@ -281,7 +282,7 @@ effectiveStdenv.mkDerivation (finalAttrs: {
     (lib.cmakeFeature "FETCHCONTENT_SOURCE_DIR_SAFEINT" "${safeint-src}")
     (lib.cmakeFeature "FETCHCONTENT_TRY_FIND_PACKAGE_MODE" "ALWAYS")
     # fails to find protoc on darwin, so specify it
-    (lib.cmakeFeature "ONNX_CUSTOM_PROTOC_EXECUTABLE" (lib.getExe protobuf))
+    (lib.cmakeFeature "ONNX_CUSTOM_PROTOC_EXECUTABLE" (lib.getExe buildPackages.protobuf))
     (lib.cmakeBool "onnxruntime_BUILD_SHARED_LIB" true)
     (lib.cmakeBool "onnxruntime_BUILD_UNIT_TESTS" finalAttrs.doCheck)
     (lib.cmakeBool "onnxruntime_USE_FULL_PROTOBUF" withFullProtobuf)
@@ -374,6 +375,8 @@ effectiveStdenv.mkDerivation (finalAttrs: {
       ../include/onnxruntime/core/providers/coreml/coreml_provider_factory.h
   '';
 
+  strictDeps = true;
+
   # See comments in `cudaPackages.nccl`
   postFixup = lib.optionalString cudaSupport ''
     remove-references-to -t "${lib.getBin cuda_nvcc}" ''${!outputLib}/lib/libonnxruntime_providers_cuda.so