diff --git a/tests/functional/flakes/init.sh b/tests/functional/flakes/init.sh
deleted file mode 100644
index 2d4c77ba1..000000000
--- a/tests/functional/flakes/init.sh
+++ /dev/null
@@ -1,87 +0,0 @@
-source ./common.sh
-
-requireGit
-
-templatesDir=$TEST_ROOT/templates
-flakeDir=$TEST_ROOT/flake
-nixpkgsDir=$TEST_ROOT/nixpkgs
-
-nix registry add --registry $registry templates git+file://$templatesDir
-nix registry add --registry $registry nixpkgs git+file://$nixpkgsDir
-
-createGitRepo $nixpkgsDir
-createSimpleGitFlake $nixpkgsDir
-
-# Test 'nix flake init'.
-createGitRepo $templatesDir
-
-cat > $templatesDir/flake.nix <<EOF
-{
-  description = "Some templates";
-
-  outputs = { self }: {
-    templates = rec {
-      trivial = {
-        path = ./trivial;
-        description = "A trivial flake";
-        welcomeText = ''
-            Welcome to my trivial flake
-        '';
-      };
-      default = trivial;
-    };
-  };
-}
-EOF
-
-mkdir $templatesDir/trivial
-
-cat > $templatesDir/trivial/flake.nix <<EOF
-{
-  description = "A flake for building Hello World";
-
-  outputs = { self, nixpkgs }: {
-    packages.$system = rec {
-      hello = nixpkgs.legacyPackages.$system.hello;
-      default = hello;
-    };
-  };
-}
-EOF
-echo a > $templatesDir/trivial/a
-echo b > $templatesDir/trivial/b
-
-git -C $templatesDir add flake.nix trivial/
-git -C $templatesDir commit -m 'Initial'
-
-nix flake check templates
-nix flake show templates
-nix flake show templates --json | jq
-
-createGitRepo $flakeDir
-(cd $flakeDir && nix flake init)
-(cd $flakeDir && nix flake init) # check idempotence
-git -C $flakeDir add flake.nix
-nix flake check $flakeDir
-nix flake show $flakeDir
-nix flake show $flakeDir --json | jq
-git -C $flakeDir commit -a -m 'Initial'
-
-# Test 'nix flake init' with benign conflicts
-createGitRepo "$flakeDir"
-echo a > $flakeDir/a
-(cd $flakeDir && nix flake init) # check idempotence
-
-# Test 'nix flake init' with conflicts
-createGitRepo "$flakeDir"
-echo b > $flakeDir/a
-pushd $flakeDir
-(! nix flake init) |& grep "refusing to overwrite existing file '$flakeDir/a'"
-popd
-git -C $flakeDir commit -a -m 'Changed'
-
-# Test 'nix flake new'.
-rm -rf $flakeDir
-nix flake new -t templates#trivial $flakeDir
-nix flake new -t templates#trivial $flakeDir # check idempotence
-nix flake check $flakeDir
diff --git a/tests/functional/meson.build b/tests/functional/meson.build
index 15471522e..12cfe3649 100644
--- a/tests/functional/meson.build
+++ b/tests/functional/meson.build
@@ -36,7 +36,6 @@ functional_tests_scripts = [
   'flakes/develop.sh',
   'flakes/develop-r8854.sh',
   'flakes/mercurial.sh',
-  'flakes/init.sh',
   'flakes/inputs.sh',
   'flakes/follow-paths.sh',
   'flakes/build-paths.sh',
diff --git a/tests/functional2/flakes/test_init.py b/tests/functional2/flakes/test_init.py
new file mode 100644
index 000000000..63daf3dea
--- /dev/null
+++ b/tests/functional2/flakes/test_init.py
@@ -0,0 +1,176 @@
+from testlib.fixtures.nix import Nix
+from testlib.fixtures.git import Git
+from testlib.fixtures.file_helper import with_files, File
+from testlib.environ import environ
+from testlib.utils import get_global_asset_pack, get_global_asset
+from pathlib import Path
+import pytest
+
+system = environ.get("system")
+
+files = {
+    "templates": get_global_asset_pack(".git")
+    | {
+        "flake.nix": File("""{
+          description = "Some templates";
+
+          outputs = { self }: {
+            templates = rec {
+              trivial = {
+                path = ./trivial;
+                description = "A trivial flake";
+                welcomeText = ''
+                    Welcome to my trivial flake
+                '';
+              };
+              default = trivial;
+            };
+          };
+        }"""),
+        "trivial": {
+            "flake.nix": File(f"""{{
+              description = "A flake for building Hello World";
+
+              outputs = {{ self, nixpkgs }}: {{
+                packages.{system} = rec {{
+                  hello = nixpkgs.legacyPackages.{system}.hello;
+                  default = hello;
+                }};
+              }};
+            }}"""),
+            "a": File("a"),
+            "b": File("b"),
+        },
+    },
+    "flake": get_global_asset_pack(".git"),
+    "nixpkgs": get_global_asset_pack(".git")
+    | {
+        "config.nix": get_global_asset("config.nix"),
+        "flake.nix": File(f"""{{
+          outputs = {{ self }}: {{
+            legacyPackages.{system}.hello =
+              with import ./config.nix;
+              mkDerivation {{
+                name = "hello";
+                buildCommand = "echo hello > $out";
+              }};
+          }};
+        }}"""),
+    },
+    "registry.json": File(""),
+}
+
+
+@pytest.fixture(autouse=True)
+def common_init(nix: Nix, files: Path, git: Git):
+    nix.settings.add_xp_feature("nix-command", "flakes")
+    nix.settings["flake-registry"] = str(files / "registry.json")
+
+    git(files / "templates", "add", "flake.nix", "trivial/")
+    git(files / "templates", "commit", "-m", "Initial")
+    git(files / "nixpkgs", "add", "flake.nix", "config.nix")
+
+    nix.nix(
+        [
+            "registry",
+            "add",
+            "--registry",
+            files / "registry.json",
+            "templates",
+            f"git+file://{files}/templates",
+        ]
+    ).run().ok()
+    nix.nix(
+        [
+            "registry",
+            "add",
+            "--registry",
+            files / "registry.json",
+            "nixpkgs",
+            f"git+file://{files}/nixpkgs",
+        ]
+    ).run().ok()
+
+
+@with_files(files)
+class TestFlakeTemplates:
+    def test_check(self, nix: Nix, files: Path):
+        assert (
+            "checking template 'templates.trivial'"
+            in nix.nix(["flake", "check", files / "templates"]).run().ok().stderr_s
+        )
+
+    def test_show(self, nix: Nix, files: Path):
+        assert (
+            "A trivial flake" in nix.nix(["flake", "show", files / "templates"]).run().ok().stdout_s
+        )
+
+    def test_show_json(self, nix: Nix, files: Path):
+        result = nix.nix(["flake", "show", files / "templates", "--json"]).run().json()
+        assert result["templates"]["default"]["description"] == "A trivial flake"
+
+    def test_init(self, nix: Nix, files: Path):
+        stderr = nix.nix(["flake", "init"], cwd=files / "flake").run().ok().stderr_s
+        assert f"wrote: {files}/flake/flake.nix" in stderr
+
+    class TestWithInit:
+        @pytest.fixture(autouse=True)
+        def init_flake(self, nix: Nix, files: Path):
+            nix.nix(["flake", "init"], cwd=files / "flake").run().ok()
+
+        def test_init_idempotent(self, nix: Nix, files: Path):
+            stderr = nix.nix(["flake", "init"], cwd=files / "flake").run().ok().stderr_s
+            assert "skipping identical file" in stderr
+
+        class TestInRepo:
+            @pytest.fixture(autouse=True)
+            def init_repo(self, files: Path, git: Git):
+                git(files / "flake", "add", "flake.nix")
+
+            def test_check(self, nix: Nix, files: Path):
+                stderr = nix.nix(["flake", "check", files / "flake"]).run().ok().stderr_s
+                assert f"fetching git input 'git+file://{files}/flake'" in stderr
+                assert f"fetching git input 'git+file://{files}/nixpkgs'" in stderr
+                assert "evaluating flake" in stderr
+
+            def test_show(self, nix: Nix, files: Path):
+                stdout = nix.nix(["flake", "show", files / "flake"]).run().ok().stdout_s
+                assert "hello: package 'hello'" in stdout
+
+            def test_show_json(self, nix: Nix, files: Path):
+                result = nix.nix(["flake", "show", files / "flake", "--json"]).run().json()
+                assert result["packages"][system]["default"]["name"] == "hello"
+                assert result["packages"][system]["hello"]["name"] == "hello"
+
+    def test_benign_conflict_idempotence(self, nix: Nix, files: Path):
+        (files / "flake/a").write_text("a")
+
+        stderr = nix.nix(["flake", "init"], cwd=files / "flake").run().ok().stderr_s
+        assert "skipping identical file" in stderr
+        assert f"wrote: {files}/flake/flake.nix" in stderr
+
+    def test_init_conflict(self, nix: Nix, files: Path):
+        (files / "flake/a").write_text("b")
+
+        stderr = nix.nix(["flake", "init"], cwd=files / "flake").run().expect(1).stderr_s
+        assert f"refusing to overwrite existing file '{files}/flake/a'" in stderr
+
+    def test_new(self, nix: Nix):
+        stderr = nix.nix(["flake", "new", "-t", "templates#trivial", "flake2"]).run().ok().stderr_s
+        assert f"wrote: {nix.env.dirs.home}/flake2/flake.nix" in stderr
+
+    class TestNew:
+        def test_idempotent(self, nix: Nix, files: Path):
+            nix.nix(["flake", "new", "-t", "templates#trivial", files / "flake2"]).run().ok()
+            stderr = (
+                nix.nix(["flake", "new", "-t", "templates#trivial", files / "flake2"])
+                .run()
+                .ok()
+                .stderr_s
+            )
+            assert "skipping identical file" in stderr
+
+        def test_check(self, nix: Nix, files: Path):
+            nix.nix(["flake", "new", "-t", "templates#trivial", files / "flake2"]).run().ok()
+            stderr = nix.nix(["flake", "check", files / "flake2"]).run().ok().stderr_s
+            assert "evaluating flake" in stderr