diff --git a/math/py-ml-dtypes/Makefile b/math/py-ml-dtypes/Makefile
index 63b27391cb34..a31198cd13d2 100644
--- a/math/py-ml-dtypes/Makefile
+++ b/math/py-ml-dtypes/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	ml-dtypes
-PORTVERSION=	0.5.1
-PORTREVISION=	2
+PORTVERSION=	0.5.4
 CATEGORIES=	math python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -18,9 +17,14 @@ BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=2.0,1<3,1:math/py-numpy@${PY_FLAVOR
 		${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=2.1.0,1:math/py-numpy@${PY_FLAVOR}
 
-USES=		python
+USES=		eigen:5 python
 USE_PYTHON=	autoplist concurrent pep517
 
+post-patch:
+	@${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|' ${WRKSRC}/setup.py
+# Clean up bundled libraries
+	@${RM} -r ${WRKSRC}/third_party/
+
 post-install:
 	${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR} -name '*.so' -exec ${STRIP_CMD} {} +
 
diff --git a/math/py-ml-dtypes/distinfo b/math/py-ml-dtypes/distinfo
index fc3946fc55a5..884509f5cd20 100644
--- a/math/py-ml-dtypes/distinfo
+++ b/math/py-ml-dtypes/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1738089116
-SHA256 (ml_dtypes-0.5.1.tar.gz) = ac5b58559bb84a95848ed6984eb8013249f90b6bab62aa5acbad876e256002c9
-SIZE (ml_dtypes-0.5.1.tar.gz) = 698772
+TIMESTAMP = 1775414472
+SHA256 (ml_dtypes-0.5.4.tar.gz) = 8ab06a50fb9bf9666dd0fe5dfb4676fa2b0ac0f31ecff72a6c3af8e22c063453
+SIZE (ml_dtypes-0.5.4.tar.gz) = 692314
diff --git a/math/py-ml-dtypes/files/patch-pyproject.toml b/math/py-ml-dtypes/files/patch-pyproject.toml
index 23cd5429a7c2..f6011ea389d5 100644
--- a/math/py-ml-dtypes/files/patch-pyproject.toml
+++ b/math/py-ml-dtypes/files/patch-pyproject.toml
@@ -1,10 +1,20 @@
---- pyproject.toml.orig	2025-01-07 02:25:37 UTC
+--- pyproject.toml.orig	2025-11-17 22:18:59 UTC
 +++ pyproject.toml
-@@ -52,7 +52,7 @@ requires = [
+@@ -4,8 +4,7 @@ requires-python = ">=3.9"
+ description = "ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used in machine learning."
+ readme = "README.md"
+ requires-python = ">=3.9"
+-license = "Apache-2.0"
+-license-files = ["LICENSE", "LICENSE.eigen"]
++license = {file = "LICENSE"}
+ authors = [{name = "ml_dtypes authors", email="ml_dtypes@google.com"}]
+ classifiers = [
+     "Programming Language :: Python :: 3",
+@@ -52,7 +51,7 @@ requires = [
      # We build against the most recent supported NumPy 2.0 release;
      # see https://github.com/numpy/numpy/issues/27265
      "numpy~=2.0",
--    "setuptools~=75.7.0",
+-    "setuptools~=80.9.0",
 +    "setuptools",
  ]
  build-backend = "setuptools.build_meta"
diff --git a/math/py-ml-dtypes/files/patch-setup.py b/math/py-ml-dtypes/files/patch-setup.py
new file mode 100644
index 000000000000..18d0c7f70609
--- /dev/null
+++ b/math/py-ml-dtypes/files/patch-setup.py
@@ -0,0 +1,11 @@
+--- setup.py.orig	2025-11-17 22:18:59 UTC
++++ setup.py
+@@ -66,7 +66,7 @@ setup(
+                 "ml_dtypes/_src/numpy.cc",
+             ],
+             include_dirs=[
+-                "third_party/eigen",
++                "%%LOCALBASE%%/include/eigen3",
+                 ".",
+                 np.get_include(),
+             ],