diff --git a/src/libflake/flakeref.cc b/src/libflake/flakeref.cc
index d56f2858f..c9e9a70ef 100644
--- a/src/libflake/flakeref.cc
+++ b/src/libflake/flakeref.cc
@@ -168,8 +168,10 @@ std::pair<FlakeRef, std::string> parsePathFlakeRefWithFragment(
                         parsedURL.query.insert_or_assign("dir", subdir);
                     }
 
-                    if (pathExists(flakeRoot + "/.git/shallow"))
-                        parsedURL.query.insert_or_assign("shallow", "1");
+                    if (!parsedURL.query.count("shallow")) {
+                       // We assume shallow by default, so we don't need to compute the revCount, which is an expensive operation.
+                       parsedURL.query.insert_or_assign("shallow", "1");
+                    }
 
                     return fromParsedURL(fetchSettings, std::move(parsedURL), isFlake);
                 }
diff --git a/tests/functional/fetchGitShallow.sh b/tests/functional/fetchGitShallow.sh
index cf7e5fd4f..7a937d9d1 100644
--- a/tests/functional/fetchGitShallow.sh
+++ b/tests/functional/fetchGitShallow.sh
@@ -65,3 +65,8 @@ fi
 # Verify that we can shallow fetch the worktree
 git -C "$TEST_ROOT/shallow-worktree" rev-list --count HEAD >/dev/null
 nix eval --impure --raw --expr "(builtins.fetchGit { url = \"file://$TEST_ROOT/shallow-worktree\"; shallow = true; }).rev"
+
+# Normal flake operation work because they use shallow by default
+pushd "$TEST_ROOT/shallow-worktree"
+nix flake metadata
+popd