diff --git a/misc/py-onnxruntime/Makefile b/misc/py-onnxruntime/Makefile
index 4d3a5c167bd4..a3ec059102f8 100644
--- a/misc/py-onnxruntime/Makefile
+++ b/misc/py-onnxruntime/Makefile
@@ -1,83 +1,76 @@
 PORTNAME=	onnxruntime
 DISTVERSIONPREFIX=	v
 DISTVERSION=	1.27.0
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	misc # machine-learning
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 DIST_SUBDIR=	${PORTNAME}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Cross-platform, high performance ML inferencing & training accelerator
 WWW=		https://onnxruntime.ai/ \
 		https://github.com/microsoft/onnxruntime
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	cmake:devel/cmake-core \
 		${PYTHON_PKGNAMEPREFIX}packaging>=0:devel/py-packaging@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numpy>=1.21.6:math/py-numpy@${PY_FLAVOR}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.21.6:math/py-numpy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}packaging>=0:devel/py-packaging@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}protobuf>=4.25.8:devel/py-protobuf@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}flatbuffers>=0:devel/py-flatbuffers@${PY_FLAVOR}
 
 USES=		compiler:c++17-lang python
 USE_PYTHON=	pep517 autoplist concurrent
 
-# Build using the official build.py script; wheel is left in ${WRKDIR}/build/Release/dist.
+# Build using the official build.py script
 PEP517_BUILD_DEPEND=
-PEP517_INSTALL_CMD=	${PYTHON_CMD} -m installer --destdir ${STAGEDIR} --prefix ${PREFIX} ${WRKDIR}/build/Release/dist/onnxruntime-${DISTVERSION}*.whl
+
+MAKE_ENV+=	ORT_DIST_DIR=${WRKSRC}/dist
 
 do-build:
 	cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \
 		${PYTHON_CMD} tools/ci_build/build.py \
 		--build_dir ${WRKDIR}/build \
 		--config Release \
 		--parallel \
 		--skip_tests \
 		--skip_submodule_sync \
 		--allow_running_as_root \
 		--enable_pybind \
 		--build_wheel \
 		--cmake_extra_defines CMAKE_INSTALL_PREFIX=${PREFIX} \
 		--cmake_extra_defines onnxruntime_BUILD_UNIT_TESTS=OFF \
 		--cmake_extra_defines ONNXRUNTIME_NUMPY_INCLUDE_DIR=${PYTHONPREFIX_SITELIBDIR}/numpy/_core/include
 
-# The upstream wheel build does not include the native pybind extension, so
-# install it alongside the pure-Python files and add it to the autoplist.
-post-install:
-	${INSTALL_DATA} ${WRKDIR}/build/Release/onnxruntime/capi/onnxruntime_pybind11_state.so \
-		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/onnxruntime/capi/
-	@${ECHO_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/onnxruntime/capi/onnxruntime_pybind11_state.so \
-		>> ${_PYTHONPKGLIST}
-
 USE_GITHUB=	yes
 GH_ACCOUNT=	microsoft
 GH_TUPLE=	emscripten-core:emsdk:0742117:emsdk/cmake/external/emsdk \
 		google:libprotobuf-mutator:7a2ed51a6b682a83e345ff49fc4cfd7ca47550db:libprotobuf_mutator/cmake/external/libprotobuf-mutator \
 		onnx:onnx:b8baa8446686496da4cc8fda09f2b6fe65c2a02c:onnx/cmake/external/onnx
 
 CXXFLAGS+=	-Wno-array-bounds # workaround for https://github.com/microsoft/onnxruntime/issues/23410
 CXXFLAGS+=	-I${WRKSRC}/include/onnxruntime/core/common/logging # otherwise logging.h isn't found
 CXXFLAGS_powerpc64le=	-Wno-error=deprecated-declarations
 
 DEPS_FILE=	${WRKSRC}/cmake/deps.txt
 
 CONFLICTS_BUILD=	abseil benchmark nsync googletest dlpack flatbuffers gsl mimalloc \
 			nlohmann-json onnx protobuf psimd pthreadpool pybind11 re2
 
 dev-update-deps-in-makefiles: extract # this should be run when the port is updated
 	@${FILESDIR}/convert-deps.sh ${DEPS_FILE}
 
 post-patch:
 	@${FIND} ${WRKSRC}/cmake/external -name "*.cmake" -exec ${REINPLACE_CMD} -e 's|--binary ||g' {} +
 
 pre-configure:
 	@${REINPLACE_CMD} -E 's|;(https://.*)/([^/]+\.zip);|;file://${DISTDIR}/${DIST_SUBDIR}/\2;|' ${DEPS_FILE}
 
 .include <Makefile.MASTER_SITES>
 .include <Makefile.DISTFILES>
 .include <bsd.port.mk>
diff --git a/misc/py-onnxruntime/files/patch-setup.py b/misc/py-onnxruntime/files/patch-setup.py
new file mode 100644
index 000000000000..69bc35ddb8ef
--- /dev/null
+++ b/misc/py-onnxruntime/files/patch-setup.py
@@ -0,0 +1,15 @@
+--- setup.py.orig	2026-08-15 00:00:00 UTC
++++ setup.py
+@@ -434,6 +434,12 @@ elif platform.system() == "Darwin":
+     libs.extend(["libonnxruntime_providers_vitisai.dylib"])
+     if nightly_build:
+         libs.extend(["libonnxruntime_pywrapper.dylib"])
++elif platform.system() == "FreeBSD":
++    libs = [
++        "onnxruntime_pybind11_state.so",
++        "libonnxruntime_providers_shared.so",
++        "libonnxruntime.so*",
++    ]
+ else:
+     libs = [
+         "onnxruntime_pybind11_state.pyd",
diff --git a/misc/py-onnxruntime/files/patch-tools_ci__build_build.py b/misc/py-onnxruntime/files/patch-tools_ci__build_build.py
new file mode 100644
index 000000000000..f4807c853eee
--- /dev/null
+++ b/misc/py-onnxruntime/files/patch-tools_ci__build_build.py
@@ -0,0 +1,11 @@
+--- tools/ci_build/build.py.orig	2026-08-15 00:00:00 UTC
++++ tools/ci_build/build.py
+@@ -1953,6 +1953,8 @@ def build_python_wheel(
+             cwd = os.path.join(cwd, config)
+
+         args = [sys.executable, os.path.join(source_dir, "setup.py"), "bdist_wheel"]
++        if os.environ.get("ORT_DIST_DIR"):
++            args.extend(["--dist-dir", os.environ["ORT_DIST_DIR"]])
+
+         # Any combination of the following arguments can be applied
+         if nightly_build: