diff --git a/xarray/core/dataset.py b/xarray/core/dataset.py
index 4f5c4fe5ddf..34acac1514f 100644
--- a/xarray/core/dataset.py
+++ b/xarray/core/dataset.py
@@ -3007,6 +3007,9 @@ def isel(
                     if drop and var.ndim == 0 and name in coord_names:
                         coord_names.remove(name)
                         continue
+                    # Update our reference to `var_dims` after the call to isel
+                    # to reflect any dropped dimensions
+                    var_dims = var.dims
             variables[name] = var
             dims.update(zip(var_dims, var.shape))