diff --git a/dev-python/cython/cython-3.0.12-r1.ebuild b/dev-python/cython/cython-3.0.12-r1.ebuild
index 07e00cd150eb5..470e50beedd26 100644
--- a/dev-python/cython/cython-3.0.12-r1.ebuild
+++ b/dev-python/cython/cython-3.0.12-r1.ebuild
@@ -44,6 +44,13 @@ 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=
diff --git a/dev-python/cython/cython-3.0.12.ebuild b/dev-python/cython/cython-3.0.12.ebuild
index b784ea2727667..2c0ca14e790f3 100644
--- a/dev-python/cython/cython-3.0.12.ebuild
+++ b/dev-python/cython/cython-3.0.12.ebuild
@@ -50,6 +50,13 @@ 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=
diff --git a/dev-python/cython/cython-3.1.0_beta1-r1.ebuild b/dev-python/cython/cython-3.1.0_beta1-r1.ebuild
index 763a686503d77..540e52b73a794 100644
--- a/dev-python/cython/cython-3.1.0_beta1-r1.ebuild
+++ b/dev-python/cython/cython-3.1.0_beta1-r1.ebuild
@@ -45,6 +45,13 @@ 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=