diff --git a/math/py-pynndescent/Makefile b/math/py-pynndescent/Makefile
index c7df0c2b53ce..a20bf472ec34 100644
--- a/math/py-pynndescent/Makefile
+++ b/math/py-pynndescent/Makefile
@@ -1,27 +1,34 @@
 PORTNAME=	pynndescent
-DISTVERSION=	0.5.13
-PORTREVISION=	3
+DISTVERSION=	0.6.0
 CATEGORIES=	math python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Python nearest neighbor descent for approximate nearest neighbors
 WWW=		https://github.com/lmcinnes/pynndescent
 
 LICENSE=	APACHE20
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}joblib>0.11:devel/py-joblib@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}llvmlite>=0.30:devel/py-llvmlite@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}numba>=0.51.2:devel/py-numba@${PY_FLAVOR} \
+BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}setuptools>61:devel/py-setuptools@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}joblib>=0.11:devel/py-joblib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}llvmlite>=0.38:devel/py-llvmlite@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numba>=0.55.0:devel/py-numba@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.18:science/py-scikit-learn@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>=1.0:science/py-scipy@${PY_FLAVOR}
 
 USES=		python
-USE_PYTHON=	distutils autoplist pytest # 1 test fails, see https://github.com/lmcinnes/pynndescent/issues/239
+USE_PYTHON=	pep517 autoplist pytest
 
 NO_ARCH=	yes
 
+TEST_ARGS=	-k 'not sokalmichener' -p no:cov -p no:black -p no:mypy
+
+# tests as of 0.6.0: 159 passed, 1 skipped in 724.95s (0:12:04)
+# sokalmichener distance tests are skipped because scikit-learn no longer
+# accepts that metric name, see https://github.com/lmcinnes/pynndescent/issues/239
+
 .include <bsd.port.mk>
diff --git a/math/py-pynndescent/distinfo b/math/py-pynndescent/distinfo
index 109a263dc925..58447a2ae590 100644
--- a/math/py-pynndescent/distinfo
+++ b/math/py-pynndescent/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1724602082
-SHA256 (pynndescent-0.5.13.tar.gz) = d74254c0ee0a1eeec84597d5fe89fedcf778593eeabe32c2f97412934a9800fb
-SIZE (pynndescent-0.5.13.tar.gz) = 2975955
+TIMESTAMP = 1785904816
+SHA256 (pynndescent-0.6.0.tar.gz) = 7ffde0fb5b400741e055a9f7d377e3702e02250616834231f6c209e39aac24f5
+SIZE (pynndescent-0.6.0.tar.gz) = 2992987
diff --git a/math/py-pynndescent/files/patch-pyproject.toml b/math/py-pynndescent/files/patch-pyproject.toml
new file mode 100644
index 000000000000..b5188c75af9d
--- /dev/null
+++ b/math/py-pynndescent/files/patch-pyproject.toml
@@ -0,0 +1,11 @@
+--- pyproject.toml.orig	2025-10-16 00:00:00 UTC
++++ pyproject.toml
+@@ -7,7 +7,7 @@
+ version = "0.6.0"
+ authors = [{name = "Leland McInnes", email = "leland.mcinnes@gmail.com"}]
+ maintainers = [{name = "Leland McInnes", email = "leland.mcinnes@gmail.com"}]
+-license = "BSD-2-Clause"
++license = {text = "BSD-2-Clause"}
+ description = "Nearest Neighbor Descent"
+ keywords = ["nearest", "neighbor", "knn", "ANN"]
+ readme = "README.rst"