diff --git a/doc/source/whatsnew/v1.2.0.rst b/doc/source/whatsnew/v1.2.0.rst
index ad5af5df710ba..fbd209d73d933 100644
--- a/doc/source/whatsnew/v1.2.0.rst
+++ b/doc/source/whatsnew/v1.2.0.rst
@@ -621,6 +621,7 @@ Indexing
 - Bug in :meth:`DataFrame.iloc` and :meth:`Series.iloc` aligning objects in ``__setitem__`` (:issue:`22046`)
 - Bug in :meth:`DataFrame.loc` did not raise ``KeyError`` when missing combination was given with ``slice(None)`` for remaining levels (:issue:`19556`)
 - Bug in :meth:`DataFrame.loc` raising ``TypeError`` when non-integer slice was given to select values from :class:`MultiIndex` (:issue:`25165`, :issue:`24263`)
+- Bug in :meth:`DataFrame.loc` returning and assigning elements in wrong order when indexer is differently ordered than the :class:`MultiIndex` to filter (:issue:`31330`, :issue:`34603`)
 - Bug in :meth:`DataFrame.loc` and :meth:`DataFrame.__getitem__`  raising ``KeyError`` when columns were :class:`MultiIndex` with only one level (:issue:`29749`)
 
 Missing
diff --git a/pandas/core/indexes/multi.py b/pandas/core/indexes/multi.py
index be0b0c5208b1c..4b67deb2d102c 100644
--- a/pandas/core/indexes/multi.py
+++ b/pandas/core/indexes/multi.py
@@ -3262,7 +3262,7 @@ def _update_indexer(
                             self._get_level_indexer(x, level=i, indexer=indexer)
                         )
                         indexers = (idxrs if indexers is None else indexers).union(
-                            idxrs
+                            idxrs, sort=False
                         )
                     except KeyError:
 
@@ -3349,6 +3349,9 @@ def _reorder_indexer(
         # order they appears in a list-like sequence
         # This mapping is then use to reorder the indexer
         for i, k in enumerate(seq):
+            if is_scalar(k):
+                # GH#34603 we want to treat a scalar the same as an all equal list
+                k = [k]
             if com.is_bool_indexer(k):
                 new_order = np.arange(n)[indexer]
             elif is_list_like(k):
@@ -3362,6 +3365,9 @@ def _reorder_indexer(
                 key_order_map[level_indexer] = np.arange(len(level_indexer))
 
                 new_order = key_order_map[self.codes[i][indexer]]
+            elif isinstance(k, slice) and k.start is None and k.stop is None:
+                # slice(None) should not determine order GH#31330
+                new_order = np.ones((n,))[indexer]
             else:
                 # For all other case, use the same order as the level
                 new_order = np.arange(n)[indexer]
diff --git a/pandas/tests/indexing/multiindex/test_loc.py b/pandas/tests/indexing/multiindex/test_loc.py
index cd6176722245b..42525fc575397 100644
--- a/pandas/tests/indexing/multiindex/test_loc.py
+++ b/pandas/tests/indexing/multiindex/test_loc.py
@@ -668,3 +668,30 @@ def test_get_loc_datetime_index():
     # Check if get_loc matches for Index and MultiIndex
     assert mi.get_loc("2001-01") == slice(0, 31, None)
     assert index.get_loc("2001-01") == slice(0, 31, None)
+
+
+def test_loc_setitem_indexer_differently_ordered():
+    # GH#34603
+    mi = MultiIndex.from_product([["a", "b"], [0, 1]])
+    df = DataFrame([[1, 2], [3, 4], [5, 6], [7, 8]], index=mi)
+
+    indexer = ("a", [1, 0])
+    df.loc[indexer, :] = np.array([[9, 10], [11, 12]])
+    expected = DataFrame([[11, 12], [9, 10], [5, 6], [7, 8]], index=mi)
+    tm.assert_frame_equal(df, expected)
+
+
+def test_loc_getitem_index_differently_ordered_slice_none():
+    # GH#31330
+    df = DataFrame(
+        [[1, 2], [3, 4], [5, 6], [7, 8]],
+        index=[["a", "a", "b", "b"], [1, 2, 1, 2]],
+        columns=["a", "b"],
+    )
+    result = df.loc[(slice(None), [2, 1]), :]
+    expected = DataFrame(
+        [[3, 4], [7, 8], [1, 2], [5, 6]],
+        index=[["a", "b", "a", "b"], [2, 2, 1, 1]],
+        columns=["a", "b"],
+    )
+    tm.assert_frame_equal(result, expected)