diff --git a/devel/py-anndata/Makefile b/devel/py-anndata/Makefile
index 1ad1407bdc8f..5a20c3e973b3 100644
--- a/devel/py-anndata/Makefile
+++ b/devel/py-anndata/Makefile
@@ -1,34 +1,34 @@
 PORTNAME=	anndata
 PORTVERSION=	0.12.10
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	devel python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	sunpoet@FreeBSD.org
 COMMENT=	Annotated data
 WWW=		https://anndata.readthedocs.io/en/latest/ \
 		https://github.com/scverse/anndata
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}hatch-vcs>=0:devel/py-hatch-vcs@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}hatchling>=0:devel/py-hatchling@${PY_FLAVOR}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}array-api-compat>=1.7.1:devel/py-array-api-compat@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}h5py>=3.8:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}legacy-api-wrap>=0:devel/py-legacy-api-wrap@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}natsort>=0:devel/py-natsort@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numpy1>=1.26:math/py-numpy1@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}packaging>=24.2:devel/py-packaging@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pandas>=2.1.0,1<3,1:math/py-pandas@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pooch>=0:devel/py-pooch@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}scipy>=1.11:science/py-scipy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>=1.12:science/py-scipy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}zarr>=2.18.4:devel/py-zarr@${PY_FLAVOR}
 
 USES=		python:3.11+
 USE_PYTHON=	autoplist concurrent pep517
 
 NO_ARCH=	yes
 
 .include <bsd.port.mk>
diff --git a/devel/py-anndata/files/patch-pyproject.toml b/devel/py-anndata/files/patch-pyproject.toml
index e2344e7e0f56..15b0d132799f 100644
--- a/devel/py-anndata/files/patch-pyproject.toml
+++ b/devel/py-anndata/files/patch-pyproject.toml
@@ -1,18 +1,11 @@
 --- pyproject.toml.orig	2020-02-02 00:00:00 UTC
 +++ pyproject.toml
-@@ -40,13 +40,13 @@ dependencies = [
-     "pandas >=2.1.0, !=2.1.2, <3",
-     "numpy>=1.26",
-     # https://github.com/scverse/anndata/issues/1434
--    "scipy >=1.12,!=1.17.0",
-+    "scipy >=1.11",
-     "h5py>=3.8",
-     "natsort",
+@@ -46,7 +46,7 @@ dependencies = [
      "packaging>=24.2",
      "array_api_compat>=1.7.1",
      "legacy-api-wrap",
 -    "zarr >=2.18.7, !=3.0.*",
 +    "zarr >=2.18.4, !=3.0.*",
  ]
  dynamic = [ "version" ]