diff --git a/devel/py-zarr/Makefile b/devel/py-zarr/Makefile
index c81dbbad9572..24882485ff22 100644
--- a/devel/py-zarr/Makefile
+++ b/devel/py-zarr/Makefile
@@ -1,30 +1,40 @@
 PORTNAME=	zarr
-DISTVERSION=	2.18.4
-PORTREVISION=	2
+DISTVERSION=	3.2.1
 CATEGORIES=	devel python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Implementation of chunked, compressed, N-dimensional arrays for Python
 WWW=		https://zarr.readthedocs.io/en/stable/
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-BUILD_DEPENDS=	${PY_SETUPTOOLS} \
-		${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}asciitree>0:graphics/py-asciitree@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}fasteners>0:devel/py-fasteners@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}numcodecs>=0.10.0:misc/py-numcodecs@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR}
-RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}fsspec>0:filesystems/py-fsspec@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR}
+BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}hatch-vcs>0:devel/py-hatch-vcs@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}hatchling>=1.29.0:devel/py-hatchling@${PY_FLAVOR}
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}donfig>=0.8:devel/py-donfig@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}google-crc32c>=1.5:devel/py-google-crc32c@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numcodecs>=0.14:misc/py-numcodecs@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numpy>=2:math/py-numpy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}packaging>=22.0:devel/py-packaging@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.13:devel/py-typing-extensions@${PY_FLAVOR}
+TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}fsspec>0:filesystems/py-fsspec@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}hypothesis>=0:devel/py-hypothesis@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numpydoc>=0:textproc/py-numpydoc@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pytest-asyncio>=0:devel/py-pytest-asyncio@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pytest-benchmark>=0:devel/py-pytest-benchmark@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pytest-xdist>=0:devel/py-pytest-xdist@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}uv>=0:devel/py-uv@${PY_FLAVOR}
 
-USES=		python
-USE_PYTHON=	pep517 autoplist pytest # 32 tests fail, see https://github.com/zarr-developers/zarr-python/issues/1819#issuecomment-2359908101
+USES=		python:3.12+
+USE_PYTHON=	pep517 autoplist pytest
 
 NO_ARCH=	yes
 
+TEST_ENV=	${MAKE_ENV} PYTHONPATH=${WRKSRC}/src
+TEST_ARGS=	--ignore ${WRKSRC}/tests/test_regression
+
+# tests as of 3.2.1: 5444 passed, 273 skipped, 7 xfailed. tests/test_regression ignored because they require uv-managed venvs unavailable in the ports test environment.
+
 .include <bsd.port.mk>
diff --git a/devel/py-zarr/distinfo b/devel/py-zarr/distinfo
index 26e816e4b201..5cbf431a1557 100644
--- a/devel/py-zarr/distinfo
+++ b/devel/py-zarr/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1734080261
-SHA256 (zarr-2.18.4.tar.gz) = 37790ededd0683ae1abe6ff90aa16c22543b3436810060f53d72c15e910c24bb
-SIZE (zarr-2.18.4.tar.gz) = 3603684
+TIMESTAMP = 1785187647
+SHA256 (zarr-3.2.1.tar.gz) = 71565b738a0e7e8ed226f0516eba8c6bb53440ad7669a8c48ebb3534a161d035
+SIZE (zarr-3.2.1.tar.gz) = 675161
diff --git a/devel/py-zarr/files/patch-pyproject.toml b/devel/py-zarr/files/patch-pyproject.toml
deleted file mode 100644
index 1a3e973ddb61..000000000000
--- a/devel/py-zarr/files/patch-pyproject.toml
+++ /dev/null
@@ -1,9 +0,0 @@
---- pyproject.toml.orig	2024-12-12 16:02:37 UTC
-+++ pyproject.toml
-@@ -1,5 +1,5 @@
- [build-system]
--requires = ["setuptools>=64", "setuptools-scm>8"]
-+requires = ["setuptools", "setuptools-scm>8"]
- build-backend = "setuptools.build_meta"
- 
-