diff --git a/science/py-phono3py/Makefile b/science/py-phono3py/Makefile
index 28d23b4d0be4..ceffdb6d33b0 100644
--- a/science/py-phono3py/Makefile
+++ b/science/py-phono3py/Makefile
@@ -1,39 +1,40 @@
 PORTNAME=	phono3py
-DISTVERSION=	3.7.0
+DISTVERSION=	3.9.0
 CATEGORIES=	science python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Software to calculate phonon-phonon interaction and related properties
 WWW=		https://phonopy.github.io/phono3py/ \
 		https://github.com/phonopy/phono3py
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 PY_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}h5py>=3.0:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}matplotlib>=2.2.2:math/py-matplotlib@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}phonopy>=2.30:science/py-phonopy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}phonopy>=2.32:science/py-phonopy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}spglib>=2.3:science/py-spglib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pyyaml>=5.3:devel/py-pyyaml@${PY_FLAVOR}
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}scikit-build-core>0:devel/py-scikit-build-core@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}nanobind>0:devel/py-nanobind@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \
 		cmake:devel/cmake-core \
 		${PY_DEPENDS}
 RUN_DEPENDS=	${PY_DEPENDS}
 
 CFLAGS+=	-fPIC
 
 USES=		blaslapack:openblas fortran localbase python
 USE_PYTHON=	pep517 cython autoplist pytest
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
+TEST_WRKSRC=	${WRKSRC}/test
 
-# tests as of 3.7.0: 141 failed, 12 passed, 5 skipped, 1 warning, 39 errors in 433.87s (0:07:13)
+# tests as of 3.9.0: 11 failed, 179 passed, 8 skipped, 6 warnings, 4 errors in 2175.15s (0:36:15), see https://github.com/phonopy/phono3py/issues/307
 # - tests fail to find mubmodules that are installed and import fine when run standalone
 
 .include <bsd.port.mk>
diff --git a/science/py-phono3py/distinfo b/science/py-phono3py/distinfo
index 978638e08932..94233b93a76a 100644
--- a/science/py-phono3py/distinfo
+++ b/science/py-phono3py/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1731827430
-SHA256 (phono3py-3.7.0.tar.gz) = 0ba4816425795f59a9de986552e0ec797d47d0775946e4285febe9c0ef1fd387
-SIZE (phono3py-3.7.0.tar.gz) = 9348298
+TIMESTAMP = 1733546847
+SHA256 (phono3py-3.9.0.tar.gz) = f93b6a74a0ba976f403cf22566ac7644a66955cf07be6a037b7f9438fb5de466
+SIZE (phono3py-3.9.0.tar.gz) = 9340513