diff --git a/lib/clanTest/flake-module.nix b/lib/clanTest/flake-module.nix
index 4e140a251..214615981 100644
--- a/lib/clanTest/flake-module.nix
+++ b/lib/clanTest/flake-module.nix
@@ -158,14 +158,26 @@ in
           '';
 
       # the test's flake.nix with locked clan-core input
-      flakeForSandbox = hostPkgs.runCommand "offline-flake-for-test-${config.name}" { } ''
-        cp -r ${config.clan.directory} $out
-        chmod +w -R $out
-        substituteInPlace $out/flake.nix \
-          --replace-fail \
-            "https://git.clan.lol/clan/clan-core/archive/main.tar.gz" \
-            "${clan-core.packages.${hostPkgs.system}.clan-core-flake}"
-      '';
+      flakeForSandbox =
+        hostPkgs.runCommand "offline-flake-for-test-${config.name}"
+          {
+            nativeBuildInputs = [ hostPkgs.nix ];
+          }
+          ''
+            cp -r ${config.clan.directory} $out
+            chmod +w -R $out
+            substituteInPlace $out/flake.nix \
+              --replace-fail \
+                "https://git.clan.lol/clan/clan-core/archive/main.tar.gz" \
+                "${clan-core.packages.${hostPkgs.system}.clan-core-flake}"
+
+            # Create a proper lock file for the test flake
+            export HOME=$(mktemp -d)
+            nix flake lock $out \
+              --extra-experimental-features 'nix-command flakes' \
+              --override-input clan-core ${clan-core.packages.${hostPkgs.system}.clan-core-flake} \
+              --override-input nixpkgs ${clan-core.inputs.nixpkgs}
+          '';
     in
     {
       imports = [
diff --git a/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py b/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py
index 62b77f5ea..fefd8a262 100644
--- a/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py
+++ b/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py
@@ -14,6 +14,7 @@ from clan_cli.tests import age_keys
 from clan_cli.tests.fixture_error import FixtureError
 from clan_cli.tests.root import CLAN_CORE
 from clan_cli.tests.temporary_dir import TEMPDIR
+from clan_lib import cmd
 from clan_lib.dirs import (
     TemplateType,
     clan_templates,
@@ -23,7 +24,7 @@ from clan_lib.dirs import (
 from clan_lib.flake import Flake
 from clan_lib.locked_open import locked_open
 from clan_lib.machines.machines import Machine
-from clan_lib.nix import nix_test_store
+from clan_lib.nix import nix_command, nix_test_store
 
 log = logging.getLogger(__name__)
 
@@ -86,6 +87,11 @@ def substitute(
     print(f"flake: {flake}")
     file.write_text(buf)
 
+    # Lock the flake after substitution if clan_core was replaced
+    if clan_core_flake:
+        flake_dir = file.parent
+        cmd.run(nix_command(["flake", "lock"]), cmd.RunOpts(cwd=flake_dir))
+
 
 class FlakeForTest(NamedTuple):
     path: Path