diff --git a/dev-python/cython/cython-3.1.1.ebuild b/dev-python/cython/cython-3.1.1.ebuild
index 3931c3e0fe2eb..51b147eecc22e 100644
--- a/dev-python/cython/cython-3.1.1.ebuild
+++ b/dev-python/cython/cython-3.1.1.ebuild
@@ -5,8 +5,9 @@ EAPI=8
 
 DISTUTILS_EXT=1
 DISTUTILS_USE_PEP517=setuptools
-PYTHON_TESTED=( python3_{11..12} )
-PYTHON_COMPAT=( "${PYTHON_TESTED[@]}" pypy3_11 python3_13{,t} python3_14{,t} )
+PYTHON_FULLY_TESTED=( python3_{11..14} )
+PYTHON_TESTED=( "${PYTHON_FULLY_TESTED[@]}" pypy3_11 )
+PYTHON_COMPAT=( "${PYTHON_TESTED[@]}" python3_{13,14}t )
 PYTHON_REQ_USE="threads(+)"
 
 inherit distutils-r1 multiprocessing pypi toolchain-funcs
@@ -21,15 +22,17 @@ HOMEPAGE="
 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"
+IUSE="test test-full"
 RESTRICT="!test? ( test )"
 
 BDEPEND="
 	${RDEPEND}
 	test? (
-		$(python_gen_cond_dep '
-			<dev-python/numpy-2[${PYTHON_USEDEP}]
-		' "${PYTHON_TESTED[@]}")
+		test-full? (
+			$(python_gen_cond_dep '
+				dev-python/numpy[${PYTHON_USEDEP}]
+			' "${PYTHON_FULLY_TESTED[@]}")
+		)
 	)
 "
 
@@ -43,13 +46,6 @@ distutils_enable_sphinx docs \
 	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=
@@ -58,6 +54,9 @@ python_compile() {
 }
 
 python_test() {
+	# PYTHON_TESTED controls whether we expect the testsuite to
+	# pass at all, while PYTHON_FULLY_TESTED allows skipping before
+	# numpy is ported (and possibly other deps in future).
 	if ! has "${EPYTHON/./_}" "${PYTHON_TESTED[@]}"; then
 		einfo "Skipping tests on ${EPYTHON} (xfail)"
 		return
@@ -67,13 +66,52 @@ python_test() {
 	unset CYTHON_FORCE_REGEN
 
 	tc-export CC
-	"${PYTHON}" runtests.py \
-		-vv \
-		-j "$(makeopts_jobs)" \
-		--work-dir "${BUILD_DIR}"/tests \
-		--no-examples \
-		--no-code-style \
-		|| die "Tests fail with ${EPYTHON}"
+
+	local testargs=(
+		-vv
+		-j "$(makeopts_jobs)"
+		--work-dir "${BUILD_DIR}"/tests
+
+		--no-examples
+		--no-code-style
+
+		# Fails to find embedded.c
+		--exclude 'embedded'
+		# coverage_installed_pkg needs dev-python/pip and doesn't like
+		# 'externally-managed' (bug #927995), but we don't really
+		# want automagic test dependencies at all, so just skip
+		# unimportant-for-us coverage tests entirely.
+		--exclude 'run.coverage*'
+		--exclude 'Cython.Coverage'
+		# Automagic on dev-python/python-tests, could add this in future
+		--exclude 'run.test_exceptions'
+		# TODO: Unpackaged dev-python/interpreters-pep-734 (interpreters_backport)
+		# This only shows up as a failure with >=3.13.
+		--exclude 'subinterpreters_threading_stress_test'
+	)
+
+	if [[ ${EPYTHON} == pypy3* ]] ; then
+		testargs+=(
+			# Recursion issue
+			--exclude 'run.if_else_expr'
+			--exclude 'run.test_patma*'
+			# Slight output difference (missing '<')
+			--exclude 'run.cpp_exception_ptr_just_handler'
+
+		)
+	fi
+
+	# Keep test-full for numpy as it's large and doesn't pass tests itself
+	# on niche arches.
+	if ! use test-full || ! has "${EPYTHON/./_}" "${PYTHON_FULLY_TESTED[@]}"; then
+		testargs+=(
+			--exclude 'run.numpy*'
+			--exclude 'run.ufunc'
+			--exclude 'numpy*'
+		)
+	fi
+
+	"${PYTHON}" runtests.py "${testargs[@]}" || die "Tests fail with ${EPYTHON}"
 }
 
 python_install_all() {
diff --git a/dev-python/cython/metadata.xml b/dev-python/cython/metadata.xml
index 4960428b8c6bf..fd01ff3d83806 100644
--- a/dev-python/cython/metadata.xml
+++ b/dev-python/cython/metadata.xml
@@ -10,6 +10,12 @@
 		language as easy as Python itself. It's based on Pyrex, but supports
 		more cutting edge functionality and optimizations.
 	</longdescription>
+	<use>
+		<flag name="test-full">
+			Run test suite in full via additional (large) test
+			dependencies, like dev-python/numpy.
+		</flag>
+	</use>
 	<upstream>
 		<remote-id type="pypi">Cython</remote-id>
 		<remote-id type="github">cython/cython</remote-id>