diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py
index 06f7338755..f289663f53 100644
--- a/src/zarr/core/array.py
+++ b/src/zarr/core/array.py
@@ -27,6 +27,7 @@
 from zarr.abc.numcodec import Numcodec, _is_numcodec
 from zarr.codecs._v2 import V2Codec
 from zarr.codecs.bytes import BytesCodec
+from zarr.codecs.transpose import TransposeCodec
 from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec
 from zarr.codecs.zstd import ZstdCodec
 from zarr.core._info import ArrayInfo
@@ -4674,6 +4675,8 @@ async def init_array(
             attributes=attributes,
         )
     else:
+        if order is not None and config is None:
+            _warn_order_kwarg()
         array_array, array_bytes, bytes_bytes = _parse_chunk_encoding_v3(
             compressors=compressors,
             filters=filters,
@@ -4681,6 +4684,15 @@ async def init_array(
             dtype=zdtype,
         )
         sub_codecs = cast("tuple[Codec, ...]", (*array_array, array_bytes, *bytes_bytes))
+
+        if order is not None and not any(isinstance(codec, TransposeCodec) for codec in sub_codecs):
+            sub_codecs = (
+                *array_array,
+                TransposeCodec(order=tuple(reversed(range(len(shape_parsed))))),
+                array_bytes,
+                *bytes_bytes,
+            )
+            config = replace(parse_array_config(config), order=order)
         # A stored chunk grid passed as chunks= / shards= (e.g. by the "keep"
         # path of from_array) becomes the stored grid verbatim, so the new
         # array preserves the source grid exactly — including trailing edges
@@ -4710,8 +4722,6 @@ async def init_array(
         else:
             codecs_out = sub_codecs
 
-        if order is not None:
-            _warn_order_kwarg()
         meta = AsyncArray._create_metadata_v3(
             shape=shape_parsed,
             dtype=zdtype,
diff --git a/tests/test_codecs/test_transpose.py b/tests/test_codecs/test_transpose.py
index 949bb72a62..25cb392c1d 100644
--- a/tests/test_codecs/test_transpose.py
+++ b/tests/test_codecs/test_transpose.py
@@ -61,6 +61,32 @@ async def test_transpose(
         assert read_data.flags["C_CONTIGUOUS"]
 
 
+@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"])
+def test_create_array_v3_order_f_preserves_fortran_output(store: Store) -> None:
+    data = np.arange(12, dtype="float32").reshape((3, 4), order="F")
+    spath = StorePath(store, "transpose_from_order")
+
+    with pytest.warns(
+        RuntimeWarning, match="The `order` keyword argument has no effect for Zarr format 3 arrays"
+    ):
+        a = zarr.create_array(
+            spath,
+            shape=data.shape,
+            chunks=data.shape,
+            dtype=data.dtype,
+            order="F",
+        )
+    a[:] = data
+
+    reopened = zarr.open_array(spath).with_config({"order": "F"})
+    read_data = np.asarray(reopened[:])
+
+    assert np.array_equal(read_data, data)
+    assert read_data.flags["F_CONTIGUOUS"]
+    assert not read_data.flags["C_CONTIGUOUS"]
+    assert any(isinstance(codec, TransposeCodec) for codec in reopened.filters)
+
+
 @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"])
 @pytest.mark.parametrize("order", [[1, 2, 0], [1, 2, 3, 0], [3, 2, 4, 0, 1]])
 def test_transpose_non_self_inverse(store: Store, order: list[int]) -> None: