diff --git a/doc/whats-new.rst b/doc/whats-new.rst
index d77422df5b4..e47a5db9d69 100644
--- a/doc/whats-new.rst
+++ b/doc/whats-new.rst
@@ -46,6 +46,8 @@ Bug fixes
   By `Jimmy Westling <https://github.com/illviljan>`_.
 - Fix incompatibility with numpy 1.20 (:issue:`6818`, :pull:`6821`)
   By `Michael Niklas <https://github.com/headtr1ck>`_.
+- Fix side effects on index coordinate metadata after aligning objects. (:issue:`6852`, :pull:`6857`)
+  By `Benoît Bovy <https://github.com/benbovy>`_.
 - Make FacetGrid.set_titles send kwargs correctly using `handle.udpate(kwargs)`.
   (:issue:`6839`, :pull:`6843`)
   By `Oliver Lopez <https://github.com/lopezvoliver>`_.
diff --git a/xarray/core/alignment.py b/xarray/core/alignment.py
index 303eb6c0ef0..cee83bd1daf 100644
--- a/xarray/core/alignment.py
+++ b/xarray/core/alignment.py
@@ -467,7 +467,7 @@ def override_indexes(self) -> None:
                 if obj_idx is not None:
                     for name, var in self.aligned_index_vars[key].items():
                         new_indexes[name] = aligned_idx
-                        new_variables[name] = var
+                        new_variables[name] = var.copy()
 
             objects[i + 1] = obj._overwrite_indexes(new_indexes, new_variables)
 
@@ -507,7 +507,7 @@ def _get_indexes_and_vars(
             if obj_idx is not None:
                 for name, var in index_vars.items():
                     new_indexes[name] = aligned_idx
-                    new_variables[name] = var
+                    new_variables[name] = var.copy()
 
         return new_indexes, new_variables
 
diff --git a/xarray/tests/test_dataset.py b/xarray/tests/test_dataset.py
index 9ea47163d05..e0bc73ec044 100644
--- a/xarray/tests/test_dataset.py
+++ b/xarray/tests/test_dataset.py
@@ -2333,6 +2333,20 @@ def test_align_str_dtype(self) -> None:
         assert_identical(expected_b, actual_b)
         assert expected_b.x.dtype == actual_b.x.dtype
 
+    @pytest.mark.parametrize("join", ["left", "override"])
+    def test_align_index_var_attrs(self, join) -> None:
+        # regression test https://github.com/pydata/xarray/issues/6852
+        # aligning two objects should have no side effect on their index variable
+        # metadata.
+
+        ds = Dataset(coords={"x": ("x", [1, 2, 3], {"units": "m"})})
+        ds_noattr = Dataset(coords={"x": ("x", [1, 2, 3])})
+
+        xr.align(ds_noattr, ds, join=join)
+
+        assert ds.x.attrs == {"units": "m"}
+        assert ds_noattr.x.attrs == {}
+
     def test_broadcast(self) -> None:
         ds = Dataset(
             {"foo": 0, "bar": ("x", [1]), "baz": ("y", [2, 3])}, {"c": ("x", [4])}