diff --git a/dev-python/cython/Manifest b/dev-python/cython/Manifest
index 8e484c3d6e72f..780b68fddd6e2 100644
--- a/dev-python/cython/Manifest
+++ b/dev-python/cython/Manifest
@@ -1,3 +1,2 @@
 DIST cython-3.0.12.tar.gz 2757617 BLAKE2B 064549e36e03424065eab081b60e2761d198490cfd4d7836ea236b833ada3962e6ed42ba1710b33418f8a31ac282cdc156ceb544ee21be80ee34b7a3d3f6c7fb SHA512 c4e85596eeea444fae983d32ce8731cc5d0d612d1f96b998db3aa7946e8be151a7ea62c6df163d875111e306c870656b82a8468dd873cacf84c7bd5671a39bc3
-DIST cython-3.1.0b1.tar.gz 3192916 BLAKE2B 13a8fa48319d9c4c8cc634d3cf5af599b867466d5de4cf3a24dd342b7812a392e854d9a6152309c6ef84a2925ebfa2257792d0f4e0c8fa36580d7138a663105a SHA512 ced9d57536d3bacd274b5edc4137d400a6182b4b7a89a28cf358f843dcbb0e0e7171fb0842441a81e1d2ac12acb6fd6a3df7018fe2a8708cb188a96cb184d799
 DIST cython-3.1.0rc1.tar.gz 3158411 BLAKE2B 44540e95b8b060956654a0d92fc4b8417088816a1e3f8fc17c8575a1cbd4b71a76cc69209d58c731281a310a9f6a7e2e711f88dc6855bc487d08056203cb04d8 SHA512 b0cefe1d4e248e6044af373088902475839ae06b5855b5b3bffdce5159a0f6e54802c24715a6f6e3242a250841c2ff1e56435b7ed3e304964af01a162f8a851a
diff --git a/dev-python/cython/cython-3.1.0_beta1-r1.ebuild b/dev-python/cython/cython-3.1.0_beta1-r1.ebuild
deleted file mode 100644
index 540e52b73a794..0000000000000
--- a/dev-python/cython/cython-3.1.0_beta1-r1.ebuild
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_EXT=1
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_TESTED=( python3_{10..12} )
-PYTHON_COMPAT=( "${PYTHON_TESTED[@]}" pypy3 pypy3_11 python3_13{,t} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1 multiprocessing pypi toolchain-funcs
-
-DESCRIPTION="A Python to C compiler"
-HOMEPAGE="
-	https://cython.org/
-	https://github.com/cython/cython/
-	https://pypi.org/project/Cython/
-"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~loong ~m68k ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux ~arm64-macos ~ppc-macos ~x64-macos ~x64-solaris"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-BDEPEND="
-	${RDEPEND}
-	test? (
-		$(python_gen_cond_dep '
-			<dev-python/numpy-2[${PYTHON_USEDEP}]
-		' "${PYTHON_TESTED[@]}")
-	)
-"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-0.29.22-spawn-multiprocessing.patch"
-	"${FILESDIR}/${PN}-0.29.23-pythran-parallel-install.patch"
-	# https://github.com/cython/cython/pull/6782
-	"${FILESDIR}/${P}-pypy3.patch"
-)
-
-distutils_enable_sphinx docs \
-	dev-python/jinja2 \
-	dev-python/sphinx-issues \
-	dev-python/sphinx-tabs
-
-python_prepare_all() {
-	# Needs dev-python/pip and doesn't like 'externally-managed' (bug #927995)
-	rm tests/run/coverage_cmd_src_pkg_layout.srctree || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	# Python gets confused when it is in sys.path before build.
-	local -x PYTHONPATH=
-
-	distutils-r1_python_compile
-}
-
-python_test() {
-	if ! has "${EPYTHON/./_}" "${PYTHON_TESTED[@]}"; then
-		einfo "Skipping tests on ${EPYTHON} (xfail)"
-		return
-	fi
-
-	# Needed to avoid confusing cache tests
-	unset CYTHON_FORCE_REGEN
-
-	tc-export CC
-	# https://github.com/cython/cython/issues/1911
-	local -x CFLAGS="${CFLAGS} -fno-strict-overflow"
-	"${PYTHON}" runtests.py \
-		-vv \
-		-j "$(makeopts_jobs)" \
-		--work-dir "${BUILD_DIR}"/tests \
-		--no-examples \
-		--no-code-style \
-		|| die "Tests fail with ${EPYTHON}"
-}
-
-python_install_all() {
-	local DOCS=( CHANGES.rst README.rst ToDo.txt USAGE.txt )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/cython/files/cython-3.1.0_beta1-pypy3.patch b/dev-python/cython/files/cython-3.1.0_beta1-pypy3.patch
deleted file mode 100644
index 9884e1b84a647..0000000000000
--- a/dev-python/cython/files/cython-3.1.0_beta1-pypy3.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From c1e709dd260b7621f36737b585dac1fd45a7704c Mon Sep 17 00:00:00 2001
-From: da-woods <dw-git@d-woods.co.uk>
-Date: Sun, 6 Apr 2025 08:43:34 +0100
-Subject: [PATCH] Fix __Pyx_Owned_Py_None usage as actual function (GH-6782)
-
-In the tracing code, we are using it like a function (i.e. casting to void to mark it unused) so it has to be a function, not just a macro.
-
-Fixes https://github.com/cython/cython/issues/6781
----
- Cython/Utility/TypeConversion.c | 6 +++++-
- 1 file changed, 5 insertions(+), 1 deletion(-)
-
-diff --git a/Cython/Utility/TypeConversion.c b/Cython/Utility/TypeConversion.c
-index b86125699c7..e085fae8eb3 100644
---- a/Cython/Utility/TypeConversion.c
-+++ b/Cython/Utility/TypeConversion.c
-@@ -103,7 +103,7 @@ static CYTHON_INLINE PyObject *__Pyx_XNewRef(PyObject *obj) {
- #endif
- }
- 
--#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
-+static CYTHON_INLINE PyObject *__Pyx_Owned_Py_None(int b);
- static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b);
- static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
- static CYTHON_INLINE int __Pyx_PyObject_IsTrueAndDecref(PyObject*);
-@@ -420,6 +420,10 @@ static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) {
-   }
- }
- 
-+static CYTHON_INLINE PyObject *__Pyx_Owned_Py_None(int b) {
-+    CYTHON_UNUSED_VAR(b);
-+    return __Pyx_NewRef(Py_None);
-+}
- 
- static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) {
-   return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False);