diff --git a/tests/functional/flakes/run.sh b/tests/functional/flakes/run.sh
deleted file mode 100644
index 10595ea12..000000000
--- a/tests/functional/flakes/run.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-source ../common.sh
-
-clearStore
-rm -rf $TEST_HOME/.cache $TEST_HOME/.config $TEST_HOME/.local
-cp ../shell-hello.nix ../config.nix $TEST_HOME
-cd $TEST_HOME
-
-cat <<EOF > flake.nix
-{
-    outputs = {self}: {
-      packages.$system.pkgAsPkg = (import ./shell-hello.nix).hello;
-      packages.$system.appAsApp = self.packages.$system.appAsApp;
-
-      apps.$system.pkgAsApp = self.packages.$system.pkgAsPkg;
-      apps.$system.appAsApp = {
-        type = "app";
-        program = "\${(import ./shell-hello.nix).hello}/bin/hello";
-      };
-    };
-}
-EOF
-nix run --no-write-lock-file .#appAsApp
-nix run --no-write-lock-file .#pkgAsPkg
-
-! nix run --no-write-lock-file .#pkgAsApp || fail "'nix run' shouldn’t accept an 'app' defined under 'packages'"
-! nix run --no-write-lock-file .#appAsPkg || fail "elements of 'apps' should be of type 'app'"
-
-clearStore
diff --git a/tests/functional/meson.build b/tests/functional/meson.build
index c76731c68..14dfb494a 100644
--- a/tests/functional/meson.build
+++ b/tests/functional/meson.build
@@ -35,7 +35,6 @@ functional_tests_scripts = [
   'flakes/flakes.sh',
   'flakes/develop.sh',
   'flakes/develop-r8854.sh',
-  'flakes/run.sh',
   'flakes/mercurial.sh',
   'flakes/circular.sh',
   'flakes/init.sh',
diff --git a/tests/functional2/flakes/assets/run/flake.nix b/tests/functional2/flakes/assets/run/flake.nix
new file mode 100644
index 000000000..31089f8b8
--- /dev/null
+++ b/tests/functional2/flakes/assets/run/flake.nix
@@ -0,0 +1,12 @@
+{
+    outputs = {self}: {
+      packages.@system@.pkgAsPkg = (import ./shell-hello.nix).hello;
+      packages.@system@.pkgAsApp = self.apps.@system@.appAsApp;
+
+      apps.@system@.appAsPkg = self.packages.@system@.pkgAsPkg;
+      apps.@system@.appAsApp = {
+        type = "app";
+        program = "${(import ./shell-hello.nix).hello}/bin/hello";
+      };
+    };
+}
diff --git a/tests/functional2/flakes/test_run.py b/tests/functional2/flakes/test_run.py
new file mode 100644
index 000000000..554da2e16
--- /dev/null
+++ b/tests/functional2/flakes/test_run.py
@@ -0,0 +1,39 @@
+from testlib.fixtures.nix import Nix
+from testlib.fixtures.file_helper import with_files
+from testlib.utils import get_global_asset, CopyTemplate
+from testlib.environ import environ
+import pytest
+
+
+@with_files(
+    {
+        "shell-hello.nix": get_global_asset("shell-hello.nix"),
+        "config.nix": get_global_asset("config.nix"),
+        "flake.nix": CopyTemplate("assets/run/flake.nix", {"system": environ.get("system")}),
+    }
+)
+class TestFlakeRun:
+    @pytest.mark.parametrize("attr", ["appAsApp", "pkgAsPkg"])
+    def test_run_succeeds(self, nix: Nix, attr: str):
+        assert (
+            "Hello World"
+            in nix.nix(["run", "--no-write-lock-file", f".#{attr}"], flake=True).run().ok().stdout_s
+        )
+
+    def test_run_pkg_as_app(self, nix: Nix):
+        assert (
+            "should have type 'derivation'"
+            in nix.nix(["run", "--no-write-lock-file", ".#pkgAsApp"], flake=True)
+            .run()
+            .expect(1)
+            .stderr_s
+        )
+
+    def test_run_app_as_pkg(self, nix: Nix):
+        assert (
+            "should have type 'app'"
+            in nix.nix(["run", "--no-write-lock-file", ".#appAsPkg"], flake=True)
+            .run()
+            .expect(1)
+            .stderr_s
+        )
diff --git a/tests/functional2/testlib/global_assets/shell-hello.nix b/tests/functional2/testlib/global_assets/shell-hello.nix
new file mode 100644
index 000000000..dfe66ef93
--- /dev/null
+++ b/tests/functional2/testlib/global_assets/shell-hello.nix
@@ -0,0 +1,42 @@
+with import ./config.nix;
+
+{
+  hello = mkDerivation {
+    name = "hello";
+    outputs = [ "out" "dev" ];
+    meta.outputsToInstall = [ "out" ];
+    buildCommand =
+      ''
+        mkdir -p $out/bin $dev/bin
+
+        cat > $out/bin/hello <<EOF
+        #! ${shell}
+        who=\$1
+        echo "Hello \''${who:-World} from $out/bin/hello"
+        EOF
+        chmod +x $out/bin/hello
+
+        cat > $dev/bin/hello2 <<EOF
+        #! ${shell}
+        echo "Hello2"
+        EOF
+        chmod +x $dev/bin/hello2
+      '';
+  };
+
+  salve-mundi = mkDerivation {
+    name = "salve-mundi";
+    outputs = [ "out" ];
+    meta.outputsToInstall = [ "out" ];
+    buildCommand =
+      ''
+        mkdir -p $out/bin
+
+        cat > $out/bin/hello <<EOF
+        #! ${shell}
+        echo "Salve Mundi from $out/bin/hello"
+        EOF
+        chmod +x $out/bin/hello
+      '';
+  };
+}