diff --git a/pkgs/tools/package-management/nix/default.nix b/pkgs/tools/package-management/nix/default.nix
index 1a49e9a4cd645..99db1764dcbea 100644
--- a/pkgs/tools/package-management/nix/default.nix
+++ b/pkgs/tools/package-management/nix/default.nix
@@ -186,6 +186,10 @@ lib.makeExtensible (
         version = "2.28.2";
         hash = "sha256-yl+hlZ/VFHIZwPIDEs4ysOYgprW4VEORfSyvScF7Cwg=";
         self_attribute_name = "nix_2_28";
+        patches = [
+          # fixes user/system registries regression: https://github.com/NixOS/nix/issues/13050
+          ./patches/0001-Revert-Actually-ignore-system-user-registries-during.patch
+        ];
       };
 
       nixComponents_git = nixDependencies.callPackage ./modular/packages.nix rec {
diff --git a/pkgs/tools/package-management/nix/patches/0001-Revert-Actually-ignore-system-user-registries-during.patch b/pkgs/tools/package-management/nix/patches/0001-Revert-Actually-ignore-system-user-registries-during.patch
new file mode 100644
index 0000000000000..c38cbb3a8011c
--- /dev/null
+++ b/pkgs/tools/package-management/nix/patches/0001-Revert-Actually-ignore-system-user-registries-during.patch
@@ -0,0 +1,51 @@
+From 8df4f5db3c71046f5deaeb913e5ec0d16f70b5a2 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= <joerg@thalheim.io>
+Date: Thu, 24 Apr 2025 14:17:18 +0200
+Subject: [PATCH] Revert "Actually ignore system/user registries during
+ locking"
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+This reverts commit a08477975d90dc0d2c9f89d2a417bedb5b266931.
+
+Signed-off-by: Jörg Thalheim <joerg@thalheim.io>
+---
+ src/libflake/flake/flakeref.cc    | 2 +-
+ tests/functional/flakes/flakes.sh | 7 -------
+ 2 files changed, 1 insertion(+), 8 deletions(-)
+
+diff --git a/src/libflake/flake/flakeref.cc b/src/libflake/flake/flakeref.cc
+index 1580c2846..6e95eb767 100644
+--- a/src/libflake/flake/flakeref.cc
++++ b/src/libflake/flake/flakeref.cc
+@@ -39,7 +39,7 @@ FlakeRef FlakeRef::resolve(
+     ref<Store> store,
+     const fetchers::RegistryFilter & filter) const
+ {
+-    auto [input2, extraAttrs] = lookupInRegistries(store, input, filter);
++    auto [input2, extraAttrs] = lookupInRegistries(store, input);
+     return FlakeRef(std::move(input2), fetchers::maybeGetStrAttr(extraAttrs, "dir").value_or(subdir));
+ }
+ 
+diff --git a/tests/functional/flakes/flakes.sh b/tests/functional/flakes/flakes.sh
+index b67a0964a..d8c9f254d 100755
+--- a/tests/functional/flakes/flakes.sh
++++ b/tests/functional/flakes/flakes.sh
+@@ -220,13 +220,6 @@ nix store gc
+ nix registry list --flake-registry "file://$registry" --refresh | grepQuiet flake3
+ mv "$registry.tmp" "$registry"
+ 
+-# Ensure that locking ignores the user registry.
+-mkdir -p "$TEST_HOME/.config/nix"
+-ln -sfn "$registry" "$TEST_HOME/.config/nix/registry.json"
+-nix flake metadata flake1
+-expectStderr 1 nix flake update --flake-registry '' --flake "$flake3Dir" | grepQuiet "cannot find flake 'flake:flake1' in the flake registries"
+-rm "$TEST_HOME/.config/nix/registry.json"
+-
+ # Test whether flakes are registered as GC roots for offline use.
+ # FIXME: use tarballs rather than git.
+ rm -rf "$TEST_HOME/.cache"
+-- 
+2.49.0
+