diff --git a/src/libflake/flake/flakeref.cc b/src/libflake/flake/flakeref.cc
index 8fd15a52d..1b7c2ff84 100644
--- a/src/libflake/flake/flakeref.cc
+++ b/src/libflake/flake/flakeref.cc
@@ -234,15 +234,16 @@ std::optional<std::pair<FlakeRef, std::string>> parseURLFlakeRef(
         return std::nullopt;
     }
 
+    const auto subdir = getOr(parsedURL.query, "dir", "");
+    parsedURL.query.erase("dir");
+
     std::string fragment;
     std::swap(fragment, parsedURL.fragment);
 
     auto input = fetchers::Input::fromURL(fetchSettings, parsedURL, isFlake);
     input.parent = baseDir;
 
-    return std::make_pair(
-        FlakeRef(std::move(input), getOr(parsedURL.query, "dir", "")),
-        fragment);
+    return std::make_pair(FlakeRef(std::move(input), subdir), fragment);
 }
 
 std::pair<FlakeRef, std::string> parseFlakeRefWithFragment(
diff --git a/tests/unit/libflake/flakeref.cc b/tests/unit/libflake/flakeref.cc
index d704a26d3..d857fbc65 100644
--- a/tests/unit/libflake/flakeref.cc
+++ b/tests/unit/libflake/flakeref.cc
@@ -21,4 +21,27 @@ namespace nix {
         ASSERT_EQ(parsed, expected);
     }
 
+    /* ----------------------------------------------------------------------------
+     * parseFlakeRef
+     * --------------------------------------------------------------------------*/
+
+    TEST(parseFlakeRef, removesDirFromInputURL) {
+        fetchers::Settings fetchSettings;
+        auto s = "git+https://localhost:8181/test/test.git?dir=subdir";
+        auto flakeref = parseFlakeRef(fetchSettings, s);
+        auto expected = "git+https://localhost:8181/test/test.git";
+        auto inputURL = flakeref.input.toURLString();
+
+        ASSERT_EQ(inputURL, expected);
+    }
+
+    TEST(parseFlakeRef, setsSubdir) {
+        fetchers::Settings fetchSettings;
+        auto s = "git+https://localhost:8181/test/test.git?dir=subdir";
+        auto flakeref = parseFlakeRef(fetchSettings, s);
+        auto expected = "subdir";
+        auto flakerefSubdir = flakeref.subdir;
+
+        ASSERT_EQ(flakerefSubdir, expected);
+    }
 }