diff --git a/xarray/backends/zarr.py b/xarray/backends/zarr.py
index 5b7e9d7af47..d59cd8fb174 100644
--- a/xarray/backends/zarr.py
+++ b/xarray/backends/zarr.py
@@ -1084,13 +1084,19 @@ def _open_existing_array(self, *, name) -> ZarrArray:
             #     - Existing variables already have their attrs included in the consolidated metadata file.
             #     - The size of dimensions can not be expanded, that would require a call using `append_dim`
             #        which is mutually exclusive with `region`
+            empty: dict[str, bool] | dict[str, dict[str, bool]]
+            if _zarr_v3():
+                empty = dict(config={"write_empty_chunks": self._write_empty})
+            else:
+                empty = dict(write_empty_chunks=self._write_empty)
+
             zarr_array = zarr.open(
                 store=(
                     self.zarr_group.store if _zarr_v3() else self.zarr_group.chunk_store
                 ),
                 # TODO: see if zarr should normalize these strings.
                 path="/".join([self.zarr_group.name.rstrip("/"), name]).lstrip("/"),
-                write_empty_chunks=self._write_empty,
+                **empty,
             )
         else:
             zarr_array = self.zarr_group[name]
@@ -1115,6 +1121,14 @@ def _create_new_array(
             else:
                 encoding["write_empty_chunks"] = self._write_empty
 
+        if _zarr_v3():
+            # zarr v3 deprecated origin and write_empty_chunks
+            # instead preferring to pass them via the config argument
+            encoding["config"] = {}
+            for c in ("write_empty_chunks", "order"):
+                if c in encoding:
+                    encoding["config"][c] = encoding.pop(c)
+
         zarr_array = self.zarr_group.create(
             name,
             shape=shape,
diff --git a/xarray/tests/test_backends.py b/xarray/tests/test_backends.py
index ab7b8298618..ec9f2fe8aef 100644
--- a/xarray/tests/test_backends.py
+++ b/xarray/tests/test_backends.py
@@ -17,7 +17,6 @@
 from collections.abc import Generator, Iterator, Mapping
 from contextlib import ExitStack
 from io import BytesIO
-from os import listdir
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, Final, Literal, cast
 from unittest.mock import patch
@@ -3698,34 +3697,54 @@ def roundtrip_dir(
 
     @pytest.mark.parametrize("consolidated", [True, False, None])
     @pytest.mark.parametrize("write_empty", [True, False, None])
-    @pytest.mark.skipif(
-        has_zarr_v3, reason="zarr-python 3.x removed write_empty_chunks"
-    )
     def test_write_empty(
-        self, consolidated: bool | None, write_empty: bool | None
+        self,
+        consolidated: bool | None,
+        write_empty: bool | None,
     ) -> None:
-        if write_empty is False:
-            expected = ["0.1.0", "1.1.0"]
+        def assert_expected_files(expected: list[str], store: str) -> None:
+            """Convenience for comparing with actual files written"""
+            ls = []
+            test_root = os.path.join(store, "test")
+            for root, _, files in os.walk(test_root):
+                ls.extend(
+                    [
+                        os.path.join(root, f).removeprefix(test_root).lstrip("/")
+                        for f in files
+                    ]
+                )
+
+            assert set(expected) == set(
+                [
+                    file.lstrip("c/")
+                    for file in ls
+                    if (file not in (".zattrs", ".zarray", "zarr.json"))
+                ]
+            )
+
+        # The zarr format is set by the `default_zarr_format`
+        # pytest fixture that acts on a superclass
+        zarr_format_3 = has_zarr_v3 and zarr.config.config["default_zarr_format"] == 3
+        if (write_empty is False) or (write_empty is None and has_zarr_v3):
+            expected = ["0.1.0"]
         else:
             expected = [
                 "0.0.0",
                 "0.0.1",
                 "0.1.0",
                 "0.1.1",
-                "1.0.0",
-                "1.0.1",
-                "1.1.0",
-                "1.1.1",
             ]
 
-        ds = xr.Dataset(
-            data_vars={
-                "test": (
-                    ("Z", "Y", "X"),
-                    np.array([np.nan, np.nan, 1.0, np.nan]).reshape((1, 2, 2)),
-                )
-            }
-        )
+        if zarr_format_3:
+            data = np.array([0.0, 0, 1.0, 0]).reshape((1, 2, 2))
+            # transform to the path style of zarr 3
+            # e.g. 0/0/1
+            expected = [e.replace(".", "/") for e in expected]
+        else:
+            # use nan for default fill_value behaviour
+            data = np.array([np.nan, np.nan, 1.0, np.nan]).reshape((1, 2, 2))
+
+        ds = xr.Dataset(data_vars={"test": (("Z", "Y", "X"), data)})
 
         if has_dask:
             ds["test"] = ds["test"].chunk(1)
@@ -3741,17 +3760,42 @@ def test_write_empty(
                 write_empty_chunks=write_empty,
             )
 
+            # check expected files after a write
+            assert_expected_files(expected, store)
+
             with self.roundtrip_dir(
                 ds,
                 store,
-                {"mode": "a", "append_dim": "Z", "write_empty_chunks": write_empty},
+                save_kwargs={
+                    "mode": "a",
+                    "append_dim": "Z",
+                    "write_empty_chunks": write_empty,
+                },
             ) as a_ds:
                 expected_ds = xr.concat([ds, ds], dim="Z")
 
-                assert_identical(a_ds, expected_ds)
-
-                ls = listdir(os.path.join(store, "test"))
-                assert set(expected) == set([file for file in ls if file[0] != "."])
+                assert_identical(a_ds, expected_ds.compute())
+                # add the new files we expect to be created by the append
+                # that was performed by the roundtrip_dir
+                if (write_empty is False) or (write_empty is None and has_zarr_v3):
+                    expected.append("1.1.0")
+                else:
+                    if not has_zarr_v3:
+                        # TODO: remove zarr3 if once zarr issue is fixed
+                        # https://github.com/zarr-developers/zarr-python/issues/2931
+                        expected.extend(
+                            [
+                                "1.1.0",
+                                "1.0.0",
+                                "1.0.1",
+                                "1.1.1",
+                            ]
+                        )
+                    else:
+                        expected.append("1.1.0")
+                if zarr_format_3:
+                    expected = [e.replace(".", "/") for e in expected]
+                assert_expected_files(expected, store)
 
     def test_avoid_excess_metadata_calls(self) -> None:
         """Test that chunk requests do not trigger redundant metadata requests.