diff --git a/doc/source/whatsnew/v2.1.1.rst b/doc/source/whatsnew/v2.1.1.rst
index 11b19b1508a71..4f1ecf3a6e666 100644
--- a/doc/source/whatsnew/v2.1.1.rst
+++ b/doc/source/whatsnew/v2.1.1.rst
@@ -18,6 +18,7 @@ Fixed regressions
 - Fixed regression in :func:`read_csv` when ``delim_whitespace`` is True (:issue:`54918`, :issue:`54931`)
 - Fixed regression in :meth:`.GroupBy.get_group` raising for ``axis=1`` (:issue:`54858`)
 - Fixed regression in :meth:`DataFrame.__setitem__` raising ``AssertionError`` when setting a :class:`Series` with a partial :class:`MultiIndex` (:issue:`54875`)
+- Fixed regression in :meth:`DataFrame.filter` not respecting the order of elements for ``filter`` (:issue:`54980`)
 - Fixed regression in :meth:`DataFrame.to_sql` not roundtripping datetime columns correctly for sqlite (:issue:`54877`)
 - Fixed regression in :meth:`MultiIndex.append` raising when appending overlapping :class:`IntervalIndex` levels (:issue:`54934`)
 - Fixed regression in :meth:`Series.drop_duplicates` for PyArrow strings (:issue:`54904`)
diff --git a/pandas/core/generic.py b/pandas/core/generic.py
index f6bf51f65049a..cea2f77c44e85 100644
--- a/pandas/core/generic.py
+++ b/pandas/core/generic.py
@@ -5701,10 +5701,12 @@ def filter(
 
         if items is not None:
             name = self._get_axis_name(axis)
+            items = Index(items).intersection(labels)
+            if len(items) == 0:
+                # Keep the dtype of labels when we are empty
+                items = items.astype(labels.dtype)
             # error: Keywords must be strings
-            return self.reindex(  # type: ignore[misc]
-                **{name: labels.intersection(items)}
-            )
+            return self.reindex(**{name: items})  # type: ignore[misc]
         elif like:
 
             def f(x) -> bool_t:
diff --git a/pandas/tests/frame/methods/test_filter.py b/pandas/tests/frame/methods/test_filter.py
index 1a2fbf8a65a55..9d5e6876bb08c 100644
--- a/pandas/tests/frame/methods/test_filter.py
+++ b/pandas/tests/frame/methods/test_filter.py
@@ -137,3 +137,17 @@ def test_filter_regex_non_string(self):
         result = df.filter(regex="STRING")
         expected = df[["STRING"]]
         tm.assert_frame_equal(result, expected)
+
+    def test_filter_keep_order(self):
+        # GH#54980
+        df = DataFrame({"A": [1, 2, 3], "B": [4, 5, 6]})
+        result = df.filter(items=["B", "A"])
+        expected = df[["B", "A"]]
+        tm.assert_frame_equal(result, expected)
+
+    def test_filter_different_dtype(self):
+        # GH#54980
+        df = DataFrame({1: [1, 2, 3], 2: [4, 5, 6]})
+        result = df.filter(items=["B", "A"])
+        expected = df[[]]
+        tm.assert_frame_equal(result, expected)