diff --git a/vllm/multimodal/utils.py b/vllm/multimodal/utils.py
index bab12fd1681a..735d8b403c15 100644
--- a/vllm/multimodal/utils.py
+++ b/vllm/multimodal/utils.py
@@ -15,7 +15,6 @@ import numpy as np
 import numpy.typing as npt
 import torch
 from PIL import Image, UnidentifiedImageError
-from typing_extensions import deprecated
 
 import vllm.envs as envs
 from vllm.connections import HTTPConnection, global_http_connection
@@ -376,39 +375,12 @@ def argsort_mm_positions(
     return [(modality, idx) for modality, idx, _ in sorted_flat_items]
 
 
-# Temporary back-compatibility for plugins that define model runner
-@deprecated("`group_mm_inputs_by_modality` is superseded by "
-            "`group_mm_kwargs_by_modality` and will be removed in v0.13. "
-            "Please use `group_mm_kwargs_by_modality` instead.")
-def group_mm_inputs_by_modality(
-    mm_inputs: list[MultiModalKwargsItems]
-) -> list[list[MultiModalKwargsItems]]:
-    if not mm_inputs:
-        return []
-
-    def modality_group_func(
-            mm_input: MultiModalKwargsItems) -> Union[str, int]:
-        # If the input has multiple modalities, return an id as the unique key
-        # for the mm_input input.
-        if len(mm_input) > 1:
-            return id(mm_input)
-
-        elif len(mm_input) == 1:
-            return next(iter(mm_input.keys()))
-
-        raise AssertionError("This line should be unreachable.")
-
-    return [
-        list(group) for _, group in groupby(mm_inputs, key=modality_group_func)
-    ]
-
-
 def group_mm_kwargs_by_modality(
     mm_kwargs: list[MultiModalKwargsItem],
     *,
     device: torch.types.Device = None,
     pin_memory: bool = False,
-    merge_by_field_config: bool = False,
+    merge_by_field_config: Optional[bool] = None,
 ) -> Iterable[tuple[str, int, BatchedTensorInputs]]:
     """Group consecutive `MultiModalKwargsItem`s from `mm_kwargs` with the same
     modality together into the same `MultiModalKwargs` instance.
@@ -421,15 +393,19 @@ def group_mm_kwargs_by_modality(
     Yields:
         A tuple `(modality, num_items, grouped_kwargs)`.
     """
+    if merge_by_field_config is None:
+        raise RuntimeError(
+            "`group_mm_kwargs_by_modality` now requires "
+            "`merge_by_field_config` arg, please update your model runner "
+            "according to https://github.com/vllm-project/vllm/pull/25676.")
+
     from vllm.multimodal.inputs import MultiModalKwargs, MultiModalKwargsItems
 
     for modality, items in groupby(mm_kwargs, key=lambda item: item.modality):
         items_lst = list(items)
 
-        # TODO: Enable `merge_by_field_config` for all models
-        # to avoid creating an extra batch dimension (except for fields
-        # that are meant to be stacked anyway).
-        # We will also need to update each model to remove `flatten_bn`.
+        # TODO: Deprecate `merge_by_field_config` once
+        # we have migrated all in-tree models
         if merge_by_field_config:
             mm_kwargs_group: BatchedTensorInputs = dict(
                 MultiModalKwargsItems.from_seq(items_lst).get_data(
diff --git a/vllm/v1/worker/gpu_input_batch.py b/vllm/v1/worker/gpu_input_batch.py
index 67fb9864b19c..7848283a9096 100644
--- a/vllm/v1/worker/gpu_input_batch.py
+++ b/vllm/v1/worker/gpu_input_batch.py
@@ -7,10 +7,9 @@ from typing import Optional, cast
 
 import numpy as np
 import torch
-from typing_extensions import deprecated
 
 from vllm.lora.request import LoRARequest
-from vllm.multimodal.inputs import MultiModalFeatureSpec, MultiModalKwargsItems
+from vllm.multimodal.inputs import MultiModalFeatureSpec
 from vllm.pooling_params import PoolingParams
 from vllm.sampling_params import SamplingParams, SamplingType
 from vllm.utils import length_from_prompt_token_ids_or_embeds, swap_dict_values
@@ -53,16 +52,6 @@ class CachedRequestState:
     def num_tokens(self) -> int:
         return self.num_prompt_tokens + len(self.output_token_ids)
 
-    # Temporary back-compatibility for plugins that define model runner
-    @property
-    @deprecated("`mm_inputs` is superseded by `mm_kwargs` and will be "
-                "removed in v0.13. Please use `mm_kwargs` instead.")
-    def mm_inputs(self) -> list[MultiModalKwargsItems]:
-        return [
-            MultiModalKwargsItems.from_seq([f.data]) for f in self.mm_features
-            if f.data is not None
-        ]
-
     def get_token_id(self, idx: int) -> int:
         if idx < self.num_prompt_tokens:
             if self.prompt_token_ids is None: