diff --git a/holoviews/element/selection.py b/holoviews/element/selection.py
index a6c8ff43ac..349c3ee667 100644
--- a/holoviews/element/selection.py
+++ b/holoviews/element/selection.py
@@ -32,10 +32,12 @@ def _get_index_selection(self, index, index_cols):
         self._index_skip = True
         if not index:
             return None, None, None
-        ds = self.clone(kdims=index_cols, new_type=Dataset)
+        clone_vdims = [vdim.name for vdim in self.vdims if vdim.name not in index_cols]
+        cols = clone_vdims + index_cols
+        ds = self.clone(kdims=index_cols, vdims=clone_vdims, new_type=Dataset)
         if len(index_cols) == 1:
             index_dim = index_cols[0]
-            vals = dim(index_dim).apply(ds.iloc[index], expanded=False)
+            vals = dim(index_dim).apply(ds.iloc[index, cols], expanded=False)
             if vals.dtype.kind == 'O' and all(isinstance(v, np.ndarray) for v in vals):
                 vals = [v for arr in vals for v in util.unique_iterator(arr)]
             expr = dim(index_dim).isin(list(util.unique_iterator(vals)))
@@ -43,7 +45,7 @@ def _get_index_selection(self, index, index_cols):
             get_shape = dim(self.dataset.get_dimension(index_cols[0]), np.shape)
             index_cols = [dim(self.dataset.get_dimension(c), np.ravel) for c in index_cols]
             vals = dim(index_cols[0], util.unique_zip, *index_cols[1:]).apply(
-                ds.iloc[index], expanded=True, flat=True
+                ds.iloc[index, cols], expanded=True, flat=True
             )
             contains = dim(index_cols[0], util.lzip, *index_cols[1:]).isin(vals, object=True)
             expr = dim(contains, np.reshape, get_shape)
diff --git a/holoviews/tests/element/test_selection.py b/holoviews/tests/element/test_selection.py
index 6c2e891019..05f8ff3418 100644
--- a/holoviews/tests/element/test_selection.py
+++ b/holoviews/tests/element/test_selection.py
@@ -30,6 +30,7 @@
 )
 from holoviews.element.comparison import ComparisonTestCase
 from holoviews.element.selection import spatial_select_columnar
+from holoviews.util.transform import dim
 
 from ..utils import dask_switcher
 
@@ -61,6 +62,29 @@
 dd_available = pytest.mark.skipif(dd is None, reason='dask.dataframe not available')
 
 
+class TestIndexExpr(ComparisonTestCase):
+
+    def setUp(self):
+        import holoviews.plotting.bokeh # noqa
+        super().setUp()
+        self._backend = Store.current_backend
+        Store.set_current_backend('bokeh')
+
+    def tearDown(self):
+        Store.current_backend = self._backend
+
+    def test_index_selection_on_id_column(self):
+        # tests issue in https://github.com/holoviz/holoviews/pull/6336
+        x, y = np.random.randn(2, 100)
+        idx = np.arange(100)
+
+        points = Points(
+            {'x': x, 'y': y, 'id': idx}, kdims=['x', 'y'], vdims=['id'], datatype=['dataframe']
+        )
+        sel, _, _ = points._get_index_selection([3, 7], ['id'])
+        assert sel == dim('id').isin([3, 7])
+
+
 class TestSelection1DExpr(ComparisonTestCase):
 
     def setUp(self):