diff --git a/direnvrc b/direnvrc
index 81fcd90..8683cf5 100644
--- a/direnvrc
+++ b/direnvrc
@@ -112,15 +112,33 @@ _nix_import_env() {
   export XDG_DATA_DIRS=$XDG_DATA_DIRS${old_xdg_data_dirs:+":"}$old_xdg_data_dirs
 }
 
+_nix_strip_escape_path() {
+  local stripped_path=${1/\//}
+  local escaped_path=${stripped_path//-/--}
+  local escaped_path=${escaped_path//\//-}
+
+  echo "$escaped_path"
+}
+
 _nix_add_gcroot() {
   local storepath=$1
   local symlink=$2
+  local escaped_symlink
+  escaped_symlink=$(_nix_strip_escape_path "$symlink")
 
-  local stripped_pwd=${2/\//}
-  local escaped_pwd=${stripped_pwd//-/--}
-  local escaped_pwd=${escaped_pwd//\//-}
   ln -fsn "$storepath" "$symlink"
-  ln -fsn "$symlink" "/nix/var/nix/gcroots/per-user/$USER/$escaped_pwd"
+  ln -fsn "$symlink" "/nix/var/nix/gcroots/per-user/$USER/$escaped_symlink"
+}
+
+_nix_clean_old_gcroots() {
+  local layout_dir=$1
+  local escaped_layout_dir
+  escaped_layout_dir=$(_nix_strip_escape_path "$layout_dir")
+
+  rm -rfv "$layout_dir/flake-inputs/"
+  rm -fv "$layout_dir"/{nix,flake}-profile*
+  rm -fv "/nix/var/nix/gcroots/per-user/$USER/$escaped_layout_dir"-flake--inputs*
+  rm -fv "/nix/var/nix/gcroots/per-user/$USER/$escaped_layout_dir"-{nix,flake}--profile*
 }
 
 _nix_argsum_suffix() {
@@ -180,6 +198,8 @@ use_flake() {
      || "$need_update" == "1"
      ]];
   then
+    _nix_clean_old_gcroots "$layout_dir"
+
     # We need to update our cache
     local tmp_profile="${layout_dir}/flake-profile.$$"
     local tmp_profile_rc
@@ -196,7 +216,6 @@ use_flake() {
 
     # also add garbage collection root for source
     local flake_input_paths
-    rm -rf "$flake_inputs"
     mkdir "$flake_inputs"
     flake_input_paths=$("${NIX_BIN_PREFIX}nix" flake archive \
       --json \
@@ -322,6 +341,8 @@ use_nix() {
      || "$need_update" -eq "1"
      ]];
   then
+    _nix_clean_old_gcroots "$layout_dir"
+
     local tmp_profile="${layout_dir}/flake-profile.$$"
     local tmp_profile_rc
 
diff --git a/tests/test_gc.py b/tests/test_gc.py
index c951f62..fefda77 100644
--- a/tests/test_gc.py
+++ b/tests/test_gc.py
@@ -38,10 +38,37 @@ def common_test(direnv_project: DirenvProject) -> None:
     assert "Executing shellHook." in out2.stderr
 
 
+def common_test_clean(direnv_project: DirenvProject) -> None:
+    testenv = str(direnv_project.dir)
+
+    out3 = run(
+        ["direnv", "exec", testenv, "hello"],
+        stderr=subprocess.PIPE,
+        check=False,
+        cwd=direnv_project.dir,
+    )
+    sys.stderr.write(out3.stderr)
+
+    files = [
+        path for path in (direnv_project.dir / ".direnv").iterdir() if path.is_file()
+    ]
+    rcs = [f for f in files if f.match("*.rc")]
+    profiles = [f for f in files if not f.match("*.rc")]
+    if len(rcs) != 1 or len(profiles) != 1:
+        print(files)
+    assert len(rcs) == 1
+    assert len(profiles) == 1
+
+
 def test_use_nix(direnv_project: DirenvProject) -> None:
     direnv_project.setup_envrc("use nix")
     common_test(direnv_project)
 
+    direnv_project.setup_envrc(
+        "use nix --argstr shellHook 'echo Executing hijacked shellHook.'"
+    )
+    common_test_clean(direnv_project)
+
 
 def test_use_flake(direnv_project: DirenvProject) -> None:
     direnv_project.setup_envrc("use flake")
@@ -55,6 +82,9 @@ def test_use_flake(direnv_project: DirenvProject) -> None:
     for symlink in inputs:
         assert symlink.is_dir()
 
+    direnv_project.setup_envrc("use flake --impure")
+    common_test_clean(direnv_project)
+
 
 if __name__ == "__main__":
     unittest.main()
diff --git a/tests/testenv/shell.nix b/tests/testenv/shell.nix
index c5c9d85..05d0a7a 100644
--- a/tests/testenv/shell.nix
+++ b/tests/testenv/shell.nix
@@ -1,14 +1,11 @@
-{ pkgs ? import <nixpkgs> {}, someArg ? null }:
+{ pkgs ? import <nixpkgs> { }, someArg ? null, shellHook ? ''
+  echo "Executing shellHook."
+'' }:
 pkgs.mkShellNoCC {
+  inherit shellHook;
+
   nativeBuildInputs = [ pkgs.hello ];
-  shellHook = ''
-    echo "Executing shellHook."
-  '';
   SHOULD_BE_SET = someArg;
 
-  passthru = {
-    subshell = pkgs.mkShellNoCC {
-      THIS_IS_A_SUBSHELL = "OK";
-    };
-  };
+  passthru = { subshell = pkgs.mkShellNoCC { THIS_IS_A_SUBSHELL = "OK"; }; };
 }