diff --git a/devel/py-scikit-build-core/Makefile b/devel/py-scikit-build-core/Makefile
index 6b18efefb24b..c2aa679e5748 100644
--- a/devel/py-scikit-build-core/Makefile
+++ b/devel/py-scikit-build-core/Makefile
@@ -1,51 +1,50 @@
 PORTNAME=	scikit-build-core
-DISTVERSION=	0.12.2
+DISTVERSION=	1.0.3
 CATEGORIES=	devel python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 DISTNAME=	${PORTNAME:S/-/_/g}-${PORTVERSION}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Build backend for CMake based projects
 WWW=		https://scikit-build-core.readthedocs.io/en/latest/ \
 		https://github.com/scikit-build/scikit-build-core
 
 LICENSE=	APACHE20
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${PY_SETUPTOOLS} \
 		${PYTHON_PKGNAMEPREFIX}hatch-fancy-pypi-readme>0:devel/py-hatch-fancy-pypi-readme@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}hatch-vcs>0:devel/py-hatch-vcs@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}hatchling>0:devel/py-hatchling@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR}
 RUN_DEPENDS=	${PY_EXCEPTIONGROUP} \
 		${PYTHON_PKGNAMEPREFIX}packaging>=23.2:devel/py-packaging@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}pathspec>=0.12.0:devel/py-pathspec@${PY_FLAVOR} \
-		${PY_TOMLI}
+		${PYTHON_PKGNAMEPREFIX}pathspec>=0.12.0:devel/py-pathspec@${PY_FLAVOR}
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}build>=0.8:devel/py-build@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}cattrs>=22.2.0:devel/py-cattrs@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}fastjsonschema>0:devel/py-fastjsonschema@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numpy>=0:math/py-numpy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pip>=23:devel/py-pip@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pybind11>=2.11:devel/py-pybind11@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pytest-subprocess>=1.5:devel/py-pytest-subprocess@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pytest-xdist>=3.1:devel/py-pytest-xdist@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}setuptools>0:devel/py-setuptools@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}validate-pyproject>0:devel/py-validate-pyproject@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}virtualenv>=20.20:devel/py-virtualenv@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}wheel>=0.40:devel/py-wheel@${PY_FLAVOR} \
 		cmake:devel/cmake-core \
 		git:devel/git \
 		ninja>0:devel/ninja
 
 USES=		python
 USE_PYTHON=	pep517 autoplist pytest
 
 TEST_ENV=	${MAKE_ENV} \
 		PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
 
 NO_ARCH=	yes
 
-# tests as of 0.12.2: 7 failed, 548 passed, 18 skipped, 10 xfailed, 16 errors in 198.39s (0:03:18), see https://github.com/scikit-build/scikit-build-core/issues/1298
+# tests as of 1.0.3: 7 failed, 1015 passed, 14 skipped, 1 warning in 228.87s (0:03:48)
 
 .include <bsd.port.mk>
diff --git a/devel/py-scikit-build-core/distinfo b/devel/py-scikit-build-core/distinfo
index 00b3edb0343e..609eec42a824 100644
--- a/devel/py-scikit-build-core/distinfo
+++ b/devel/py-scikit-build-core/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1778010087
-SHA256 (scikit_build_core-0.12.2.tar.gz) = 562e0bbc9de1a354c87825ccf732080268d6582a0200f648e8c4a2dcb1e3736d
-SIZE (scikit_build_core-0.12.2.tar.gz) = 303553
+TIMESTAMP = 1784564784
+SHA256 (scikit_build_core-1.0.3.tar.gz) = a4d7a05978ee37975c37743510c8991e2debce7ef83afb0a07c0c576fd4f16e8
+SIZE (scikit_build_core-1.0.3.tar.gz) = 477539
diff --git a/devel/py-scikit-build-core/files/patch-pyproject.toml b/devel/py-scikit-build-core/files/patch-pyproject.toml
new file mode 100644
index 000000000000..8b7db8717d99
--- /dev/null
+++ b/devel/py-scikit-build-core/files/patch-pyproject.toml
@@ -0,0 +1,13 @@
+-- Ignore pytest_benchmark.logger.PytestBenchmarkWarning which occurs when using pytest-xdist.
+-- This warning is not indicative of a test failure, just that benchmarks are disabled in parallel mode.
+
+--- pyproject.toml.orig2026-04-30 16:02:41 UTC
++++ pyproject.toml
+@@ -177,6 +177,7 @@ filterwarnings = [
+     "ignore::scikit_build_core._vendor.pyproject_metadata.errors.ConfigurationWarning",
+     "ignore:'_UnionGenericAlias' is deprecated and slated for removal in Python 3.17:DeprecationWarning",  # From cattrs 24.1.2 and other?
+     "ignore:The 'wheel.metadata' package has been made private:DeprecationWarning",
++    "ignore::pytest_benchmark.logger.PytestBenchmarkWarning",
+     "ignore:version of cmake-example already set:UserWarning",  # Caused by setuptoools-scm 9+ being installed
+ ]
+ log_level = "INFO"