diff --git a/xarray/core/groupby.py b/xarray/core/groupby.py
index 57802c199e1..a5482c5a514 100644
--- a/xarray/core/groupby.py
+++ b/xarray/core/groupby.py
@@ -828,7 +828,7 @@ def groups(self) -> dict[GroupKey, GroupIndex]:
             self._groups = dict(
                 zip(
                     self.encoded.unique_coord.data,
-                    self.encoded.group_indices,
+                    tuple(g for g in self.encoded.group_indices if g),
                     strict=True,
                 )
             )
diff --git a/xarray/tests/test_groupby.py b/xarray/tests/test_groupby.py
index 202b729abcf..336a5e6c91c 100644
--- a/xarray/tests/test_groupby.py
+++ b/xarray/tests/test_groupby.py
@@ -3200,6 +3200,16 @@ def test_multiple_grouper_unsorted_order() -> None:
     assert_identical(actual2, expected2)
 
 
+def test_multiple_grouper_empty_groups() -> None:
+    ds = xr.Dataset(
+        {"foo": (("x", "y"), np.random.rand(4, 3))},
+        coords={"x": [10, 20, 30, 40], "letters": ("x", list("abba"))},
+    )
+
+    groups = ds.groupby(x=BinGrouper(bins=[5, 15, 25]), letters=UniqueGrouper())
+    assert len(groups.groups) == 2
+
+
 def test_groupby_multiple_bin_grouper_missing_groups() -> None:
     from numpy import nan