diff --git a/pkgs/development/python-modules/keras/default.nix b/pkgs/development/python-modules/keras/default.nix
index 4b871998f851..61713c18972b 100644
--- a/pkgs/development/python-modules/keras/default.nix
+++ b/pkgs/development/python-modules/keras/default.nix
@@ -14,6 +14,7 @@
   ml-dtypes,
   namex,
   numpy,
+  tf2onnx,
   onnxruntime,
   optree,
   packaging,
@@ -30,18 +31,19 @@
   pytestCheckHook,
   tf-keras,
   torch,
+  writableTmpDirAsHomeHook,
 }:
 
 buildPythonPackage rec {
   pname = "keras";
-  version = "3.8.0";
+  version = "3.9.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "keras-team";
     repo = "keras";
     tag = "v${version}";
-    hash = "sha256-sbAGiI1Ai0MPiQ8AMpa5qX6hYt/plsIqhn9xYLBb120=";
+    hash = "sha256-T1QY1GwE0X5ARtAueB6kF310kTaeOA+8Obdzx0NrOUs=";
   };
 
   build-system = [
@@ -54,6 +56,7 @@ buildPythonPackage rec {
     ml-dtypes
     namex
     numpy
+    tf2onnx
     onnxruntime
     optree
     packaging
@@ -75,40 +78,26 @@ buildPythonPackage rec {
     pytestCheckHook
     tf-keras
     torch
+    writableTmpDirAsHomeHook
   ];
 
-  preCheck = ''
-    export HOME=$(mktemp -d)
-  '';
+  disabledTests = [
+    # Tries to install the package in the sandbox
+    "test_keras_imports"
 
-  disabledTests =
-    [
-      # Requires onnx which is currently broken
-      "test_export_onnx"
-
-      # Tries to install the package in the sandbox
-      "test_keras_imports"
-
-      # TypeError: this __dict__ descriptor does not support '_DictWrapper' objects
-      "test_reloading_default_saved_model"
-
-      # ValueError: The truth value of an empty array is ambiguous.
-      # Use `array.size > 0` to check that an array is not empty.
-      "test_min_max_norm"
-    ]
-    ++ lib.optionals stdenv.isDarwin [
-      # TypeError: Cannot convert a MPS Tensor to float64 dtype as the MPS framework doesn't support float64. Please use float32 instead.
-      "test_dynamic_backend_torch"
-      # AttributeError: module 'numpy' has no attribute 'float128'. Did you mean: 'float16'?
-      "test_spectrogram_error"
-    ];
+    # TypeError: this __dict__ descriptor does not support '_DictWrapper' objects
+    "test_reloading_default_saved_model"
+  ];
 
   disabledTestPaths = [
-    # Require onnx which is currently broken
+    # These tests succeed when run individually, but crash within the full test suite:
+    # ImportError: /nix/store/4bw0x7j3wfbh6i8x3plmzknrdwdzwfla-abseil-cpp-20240722.1/lib/libabsl_cord_internal.so.2407.0.0:
+    # undefined symbol: _ZN4absl12lts_2024072216strings_internal13StringifySink6AppendESt17basic_string_viewIcSt11char_traitsIcEE
     "keras/src/export/onnx_test.py"
 
-    # Datasets are downloaded from the internet
+    # Require internet access
     "integration_tests/dataset_tests"
+    "keras/src/applications/applications_test.py"
 
     # TypeError: test_custom_fit.<locals>.CustomModel.train_step() missing 1 required positional argument: 'data'
     "integration_tests/jax_custom_fit_test.py"
@@ -124,14 +113,8 @@ buildPythonPackage rec {
     # AssertionError: 0 != 2
     "integration_tests/torch_workflow_test.py"
 
-    # Most tests require internet access
-    "keras/src/applications/applications_test.py"
-
     # TypeError: this __dict__ descriptor does not support '_DictWrapper' objects
     "keras/src/backend/tensorflow/saved_model_test.py"
-
-    # KeyError: 'Unable to synchronously open object (bad object header version number)'
-    "keras/src/saving/file_editor_test.py"
   ];
 
   meta = {
diff --git a/pkgs/development/python-modules/tf2onnx/default.nix b/pkgs/development/python-modules/tf2onnx/default.nix
index cd904628903a..35ba5f495a0c 100644
--- a/pkgs/development/python-modules/tf2onnx/default.nix
+++ b/pkgs/development/python-modules/tf2onnx/default.nix
@@ -2,29 +2,25 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  # runtime dependencies
+
+  # build-system
+  setuptools,
+
+  # dependencies
+  flatbuffers,
   numpy,
   onnx,
+  onnxruntime,
+  protobuf,
   requests,
   six,
-  flatbuffers,
-  protobuf,
   tensorflow,
-  # check dependencies
-  pytestCheckHook,
-  graphviz,
-  parameterized,
-  pytest-cov-stub,
-  pyyaml,
-  timeout-decorator,
-  onnxruntime,
-  keras,
 }:
 
 buildPythonPackage rec {
   pname = "tf2onnx";
   version = "1.16.1";
-  format = "setuptools";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "onnx";
@@ -38,49 +34,36 @@ buildPythonPackage rec {
       --replace-fail "'pytest-runner'" ""
   '';
 
-  pythonRelaxDeps = [ "flatbuffers" ];
+  build-system = [
+    setuptools
+  ];
 
-  propagatedBuildInputs = [
+  pythonRelaxDeps = [
+    "protobuf"
+  ];
+
+  dependencies = [
+    flatbuffers
     numpy
     onnx
+    onnxruntime
+    protobuf
     requests
     six
-    flatbuffers
-    protobuf
     tensorflow
-    onnxruntime
   ];
 
   pythonImportsCheck = [ "tf2onnx" ];
 
-  nativeCheckInputs = [
-    pytestCheckHook
-    graphviz
-    parameterized
-    pytest-cov-stub
-    pyyaml
-    timeout-decorator
-    keras
-  ];
+  # All tests fail at import with:
+  # AttributeError: `...` is not available with Keras 3.
+  doCheck = false;
 
-  # TODO investigate the failures
-  disabledTestPaths = [
-    "tests/test_backend.py"
-    "tests/test_einsum_helper.py"
-    "tests/test_einsum_optimizers.py"
-  ];
-
-  disabledTests = [ "test_profile_conversion_time" ];
-
-  meta = with lib; {
+  meta = {
     description = "Convert TensorFlow, Keras, Tensorflow.js and Tflite models to ONNX";
     homepage = "https://github.com/onnx/tensorflow-onnx";
-    license = licenses.asl20;
-    maintainers = with maintainers; [ happysalada ];
-    # Duplicated `protobuf` in the derivation:
-    # - version 4.24.4 (from onnx), the default version of protobuf in nixpkgs
-    # - version 4.21.12 (from tensorflow), pinned as such because tensorflow is outdated and does
-    #   not support more recent versions of protobuf
-    broken = true;
+    changelog = "https://github.com/onnx/tensorflow-onnx/releases/tag/v${version}";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ happysalada ];
   };
 }