diff --git a/xarray/backends/zarr.py b/xarray/backends/zarr.py
index 13b1819f206..b4369fa728d 100644
--- a/xarray/backends/zarr.py
+++ b/xarray/backends/zarr.py
@@ -623,7 +623,12 @@ def store(
             # avoid needing to load index variables into memory.
             # TODO: consider making loading indexes lazy again?
             existing_vars, _, _ = conventions.decode_cf_variables(
-                self.get_variables(), self.get_attrs()
+                {
+                    k: v
+                    for k, v in self.get_variables().items()
+                    if k in existing_variable_names
+                },
+                self.get_attrs(),
             )
             # Modified variables must use the same encoding as the store.
             vars_with_encoding = {}
diff --git a/xarray/tests/test_backends.py b/xarray/tests/test_backends.py
index 07573066568..248c873d50f 100644
--- a/xarray/tests/test_backends.py
+++ b/xarray/tests/test_backends.py
@@ -2261,7 +2261,6 @@ def test_write_uneven_dask_chunks(self) -> None:
         original = create_test_data().chunk({"dim1": 3, "dim2": 4, "dim3": 3})
         with self.roundtrip(original, open_kwargs={"chunks": {}}) as actual:
             for k, v in actual.data_vars.items():
-                print(k)
                 assert v.chunks == actual[k].chunks
 
     def test_chunk_encoding(self) -> None:
@@ -2468,6 +2467,27 @@ def test_group(self) -> None:
         ) as actual:
             assert_identical(original, actual)
 
+    def test_zarr_mode_w_overwrites_encoding(self) -> None:
+        import zarr
+
+        data = Dataset({"foo": ("x", [1.0, 1.0, 1.0])})
+        with self.create_zarr_target() as store:
+            data.to_zarr(
+                store, **self.version_kwargs, encoding={"foo": {"add_offset": 1}}
+            )
+            np.testing.assert_equal(
+                zarr.open_group(store, **self.version_kwargs)["foo"], data.foo.data - 1
+            )
+            data.to_zarr(
+                store,
+                **self.version_kwargs,
+                encoding={"foo": {"add_offset": 0}},
+                mode="w",
+            )
+            np.testing.assert_equal(
+                zarr.open_group(store, **self.version_kwargs)["foo"], data.foo.data
+            )
+
     def test_encoding_kwarg_fixed_width_string(self) -> None:
         # not relevant for zarr, since we don't use EncodedStringCoder
         pass