diff --git a/pkgs/applications/misc/prusa-slicer/default.nix b/pkgs/applications/misc/prusa-slicer/default.nix
index de0e544b8054..8430f97901cd 100644
--- a/pkgs/applications/misc/prusa-slicer/default.nix
+++ b/pkgs/applications/misc/prusa-slicer/default.nix
@@ -35,6 +35,7 @@
   heatshrink,
   catch2,
   webkitgtk_4_0,
+  ctestCheckHook,
   withSystemd ? lib.meta.availableOn stdenv.hostPlatform systemd,
   systemd,
   wxGTK-override ? null,
@@ -205,16 +206,12 @@ stdenv.mkDerivation (finalAttrs: {
   '';
 
   doCheck = true;
-
-  checkPhase = ''
-    runHook preCheck
-
-    ctest \
-      --force-new-ctest-process \
-      -E 'libslic3r_tests|sla_print_tests'
-
-    runHook postCheck
-  '';
+  nativeCheckInputs = [ ctestCheckHook ];
+  checkFlags = [
+    "--force-new-ctest-process"
+    "-E"
+    "libslic3r_tests|sla_print_tests"
+  ];
 
   meta =
     with lib;
diff --git a/pkgs/by-name/al/alembic/package.nix b/pkgs/by-name/al/alembic/package.nix
index 091edf349412..08a804fa1514 100644
--- a/pkgs/by-name/al/alembic/package.nix
+++ b/pkgs/by-name/al/alembic/package.nix
@@ -60,11 +60,7 @@ stdenv.mkDerivation rec {
   '';
 
   doCheck = true;
-  checkPhase = ''
-    runHook preCheck
-    ctest -j 1
-    runHook postCheck
-  '';
+  enableParallelChecking = false;
 
   meta = with lib; {
     description = "Open framework for storing and sharing scene data";
diff --git a/pkgs/by-name/cc/ccache/package.nix b/pkgs/by-name/cc/ccache/package.nix
index 29a286570bae..00162a46eb58 100644
--- a/pkgs/by-name/cc/ccache/package.nix
+++ b/pkgs/by-name/cc/ccache/package.nix
@@ -15,6 +15,8 @@
   doctest,
   xcodebuild,
   makeWrapper,
+  ctestCheckHook,
+  writableTmpDirAsHomeHook,
   nix-update-script,
 }:
 
@@ -82,31 +84,24 @@ stdenv.mkDerivation (finalAttrs: {
     # test/run requires the compgen function which is available in
     # bashInteractive, but not bash.
     bashInteractive
+    ctestCheckHook
+    writableTmpDirAsHomeHook
   ] ++ lib.optional stdenv.hostPlatform.isDarwin xcodebuild;
 
   checkInputs = [
     doctest
   ];
 
-  checkPhase =
-    let
-      badTests =
-        [
-          "test.trim_dir" # flaky on hydra (possibly filesystem-specific?)
-        ]
-        ++ lib.optionals stdenv.hostPlatform.isDarwin [
-          "test.basedir"
-          "test.fileclone" # flaky on hydra (possibly filesystem-specific?)
-          "test.multi_arch"
-          "test.nocpp2"
-        ];
-    in
-    ''
-      runHook preCheck
-      export HOME=$(mktemp -d)
-      ctest --output-on-failure -E '^(${lib.concatStringsSep "|" badTests})$'
-      runHook postCheck
-    '';
+  disabledTests =
+    [
+      "test.trim_dir" # flaky on hydra (possibly filesystem-specific?)
+      "test.fileclone" # flaky on hydra, also seems to fail on zfs
+    ]
+    ++ lib.optionals stdenv.hostPlatform.isDarwin [
+      "test.basedir"
+      "test.multi_arch"
+      "test.nocpp2"
+    ];
 
   passthru = {
     # A derivation that provides gcc and g++ commands, but that
diff --git a/pkgs/by-name/ez/eztrace/package.nix b/pkgs/by-name/ez/eztrace/package.nix
index a55d917bfde2..6c5a82dde4a1 100644
--- a/pkgs/by-name/ez/eztrace/package.nix
+++ b/pkgs/by-name/ez/eztrace/package.nix
@@ -9,6 +9,7 @@
   libbfd,
   libopcodes,
   otf2,
+  ctestCheckHook,
   versionCheckHook,
 }:
 
@@ -54,8 +55,6 @@ stdenv.mkDerivation (finalAttrs: {
 
   cmakeFlags = [
     (lib.cmakeBool "EZTRACE_ENABLE_MEMORY" true)
-    # This test is somewhat flaky and fails once per several rebuilds.
-    (lib.cmakeFeature "CMAKE_CTEST_ARGUMENTS" "--exclude-regex;memory_tests")
   ];
 
   nativeBuildInputs = [
@@ -72,8 +71,13 @@ stdenv.mkDerivation (finalAttrs: {
   ];
 
   doCheck = true;
+  disabledTests = [
+    # This test is somewhat flaky and fails once per several rebuilds.
+    "memory_tests"
+  ];
   nativeCheckInputs = [
     otf2 # `otf2-print` needed by compiler_instrumentation_tests,pthread_tests,posixio_tests
+    ctestCheckHook
   ];
 
   postInstall = ''
diff --git a/pkgs/by-name/op/openscad-unstable/package.nix b/pkgs/by-name/op/openscad-unstable/package.nix
index 7ee708b69605..280f4035a5ce 100644
--- a/pkgs/by-name/op/openscad-unstable/package.nix
+++ b/pkgs/by-name/op/openscad-unstable/package.nix
@@ -41,6 +41,7 @@
   xorg,
   mimalloc,
   opencsg,
+  ctestCheckHook,
 }:
 # clang consume much less RAM than GCC
 clangStdenv.mkDerivation rec {
@@ -142,12 +143,16 @@ clangStdenv.mkDerivation rec {
 
   nativeCheckInputs = [
     mesa.llvmpipeHook
+    ctestCheckHook
   ];
 
-  checkPhase = ''
+  dontUseNinjaCheck = true;
+  checkFlags = [
+    "-E"
     # some fontconfig issues cause pdf output to have wrong font
-    ctest -j$NIX_BUILD_CORES -E pdfexporttest.\*
-  '';
+    "pdfexporttest"
+  ];
+
   meta = with lib; {
     description = "3D parametric model compiler (unstable)";
     longDescription = ''
diff --git a/pkgs/by-name/si/sirius/package.nix b/pkgs/by-name/si/sirius/package.nix
index df4a5a6af8a8..a913e2e9c864 100644
--- a/pkgs/by-name/si/sirius/package.nix
+++ b/pkgs/by-name/si/sirius/package.nix
@@ -6,6 +6,7 @@
   pkg-config,
   mpi,
   mpiCheckPhaseHook,
+  ctestCheckHook,
   gfortran,
   blas,
   lapack,
@@ -152,16 +153,14 @@ stdenv.mkDerivation rec {
   # Can not run parallel checks generally as it requires exactly multiples of 4 MPI ranks
   # Even cpu_serial tests had to be disabled as they require scalapack routines in the sandbox
   # and run into the same problem as MPI tests
-  checkPhase = ''
-    runHook preCheck
-
-    ctest --output-on-failure --label-exclude integration_test
-
-    runHook postCheck
-  '';
+  checkFlags = [
+    "--label-exclude"
+    "integration_test"
+  ];
 
   nativeCheckInputs = [
     mpiCheckPhaseHook
+    ctestCheckHook
   ];
 
   meta = with lib; {
diff --git a/pkgs/development/compilers/halide/default.nix b/pkgs/development/compilers/halide/default.nix
index 3ce25abaf53c..821459bacdae 100644
--- a/pkgs/development/compilers/halide/default.nix
+++ b/pkgs/development/compilers/halide/default.nix
@@ -22,6 +22,7 @@
   wasmSupport ? false,
   wabt,
   doCheck ? true,
+  ctestCheckHook,
 }:
 
 assert blas.implementation == "openblas" && lapack.implementation == "openblas";
@@ -102,15 +103,9 @@ stdenv.mkDerivation (finalAttrs: {
     "correctness_cross_compilation"
     "correctness_simd_op_check_hvx"
   ];
-  # ninja's setup-hook doesn't let us specify custom flags for the checkPhase, see
-  # https://discourse.nixos.org/t/building-only-specific-targets-with-cmake/31545/4
-  # so we resort to overriding the whole checkPhase
+
   dontUseNinjaCheck = true;
-  checkPhase = ''
-    runHook preCheck
-    ctest --exclude-regex '^(${lib.strings.concatStringsSep "|" finalAttrs.disabledTests})$'
-    runHook postCheck
-  '';
+  nativeCheckInputs = [ ctestCheckHook ];
 
   postInstall =
     lib.optionalString pythonSupport ''
diff --git a/pkgs/development/libraries/eccodes/default.nix b/pkgs/development/libraries/eccodes/default.nix
index 73e55f8f2979..6ca3c51412c8 100644
--- a/pkgs/development/libraries/eccodes/default.nix
+++ b/pkgs/development/libraries/eccodes/default.nix
@@ -9,6 +9,7 @@
   libpng,
   gfortran,
   perl,
+  ctestCheckHook,
   enablePython ? false,
   pythonPackages,
   enablePosixThreads ? false,
@@ -65,11 +66,12 @@ stdenv.mkDerivation rec {
   ];
 
   doCheck = true;
-
-  # Only do tests that don't require downloading 120MB of testdata
-  checkPhase = ''
-    ctest -R "eccodes_t_(definitions|calendar|unit_tests|md5|uerra|grib_2nd_order_numValues|julian)" -VV
-  '';
+  nativeCheckInputs = [ ctestCheckHook ];
+  checkFlags = [
+    "-R"
+    # Only do tests that don't require downloading 120MB of testdata
+    "eccodes_t_(definitions|calendar|unit_tests|md5|uerra|grib_2nd_order_numValues|julian)"
+  ];
 
   meta = with lib; {
     homepage = "https://confluence.ecmwf.int/display/ECC/";