diff --git a/src/axolotl/prompt_strategies/chat_template.py b/src/axolotl/prompt_strategies/chat_template.py
index a9d26a650..ced8c8da6 100644
--- a/src/axolotl/prompt_strategies/chat_template.py
+++ b/src/axolotl/prompt_strategies/chat_template.py
@@ -379,6 +379,22 @@ class ChatTemplateStrategy(PromptTokenizingStrategy):
         Public method that can handle either a single prompt or a batch of prompts.
         """
 
+        def _remove_none_values(obj):
+            """
+            Remove null from a dictionary-like obj or list.
+            These can appear due to Dataset loading causing schema merge.
+            See https://github.com/axolotl-ai-cloud/axolotl/pull/2909
+            """
+            if hasattr(obj, "items"):
+                return {
+                    k: _remove_none_values(v) for k, v in obj.items() if v is not None
+                }
+            if isinstance(obj, list):
+                return [_remove_none_values(elem) for elem in obj]
+            return obj
+
+        prompt = _remove_none_values(prompt)
+
         if not self.is_prompt_batched(prompt) or not self.supports_batched:
             return self._tokenize_single_prompt(prompt)
 
diff --git a/tests/prompt_strategies/test_chat_template_ds_schema_unification.py b/tests/prompt_strategies/test_chat_template_ds_schema_unification.py
new file mode 100644
index 000000000..502efae4b
--- /dev/null
+++ b/tests/prompt_strategies/test_chat_template_ds_schema_unification.py
@@ -0,0 +1,75 @@
+"""
+Tests for chat template prompt strategy with schema unification for none fields
+"""
+
+import json
+
+import pytest
+from datasets import Dataset
+from transformers import AutoTokenizer
+
+from axolotl.prompt_strategies.chat_template import StrategyLoader
+from axolotl.utils.dict import DictDefault
+
+
+@pytest.fixture(name="messages_w_tools")
+def fixture_messages_w_tools():
+    jsons = """
+{"messages":[{"role":"user","content":"move to (0, 1)"},{"role":"assistant","content":"","tool_calls":[{"function":{"name":"move","arguments":{"x":0,"y":1}}}]}],"tools":[{"type":"function","function":{"name":"move","description":"Move to a given location measured in meters","parameters":{"type":"object","properties":{"x":{"type":"number","description":"The x coordinate of the location, negative values are to the left, positive values are to the right"},"y":{"type":"number","description":"The y coordinate of the location, negative values are backward, positive values are forward"}},"required":["x","y"]}}},{"type":"function","function":{"name":"turn","description":"Turn the robot to a given direction","parameters":{"type":"object","properties":{"theta":{"type":"integer","description":"The angle to turn to, in degrees, positive values are counter-clockwise, negative values are clockwise"}},"required":["theta"]}}},{"type":"function","function":{"name":"invalid_prompt","description":"call when the user's prompt is invalid","parameters":{"type":"object","properties":{"message":{"type":"string","description":"why the prompt is invalid"}},"required":["message"]}}}],"add_generation_prompt":false}
+{"messages":[{"role":"user","content":"turn 270 degree"},{"role":"assistant","content":"","tool_calls":[{"function":{"name":"turn","arguments":{"theta": 270}}}]}],"tools":[{"type":"function","function":{"name":"move","description":"Move to a given location measured in meters","parameters":{"type":"object","properties":{"x":{"type":"number","description":"The x coordinate of the location, negative values are to the left, positive values are to the right"},"y":{"type":"number","description":"The y coordinate of the location, negative values are backward, positive values are forward"}},"required":["x","y"]}}},{"type":"function","function":{"name":"turn","description":"Turn the robot to a given direction","parameters":{"type":"object","properties":{"theta":{"type":"integer","description":"The angle to turn to, in degrees, positive values are counter-clockwise, negative values are clockwise"}},"required":["theta"]}}},{"type":"function","function":{"name":"invalid_prompt","description":"call when the user's prompt is invalid","parameters":{"type":"object","properties":{"message":{"type":"string","description":"why the prompt is invalid"}},"required":["message"]}}}],"add_generation_prompt":false}
+{"messages":[{"role":"user","content":"jump high"},{"role":"assistant","content":"","tool_calls":[{"function":{"name":"invalid_prompt","arguments":{"message": "jump is not a valid action"}}}]}],"tools":[{"type":"function","function":{"name":"move","description":"Move to a given location measured in meters","parameters":{"type":"object","properties":{"x":{"type":"number","description":"The x coordinate of the location, negative values are to the left, positive values are to the right"},"y":{"type":"number","description":"The y coordinate of the location, negative values are backward, positive values are forward"}},"required":["x","y"]}}},{"type":"function","function":{"name":"turn","description":"Turn the robot to a given direction","parameters":{"type":"object","properties":{"theta":{"type":"integer","description":"The angle to turn to, in degrees, positive values are counter-clockwise, negative values are clockwise"}},"required":["theta"]}}},{"type":"function","function":{"name":"invalid_prompt","description":"call when the user's prompt is invalid","parameters":{"type":"object","properties":{"message":{"type":"string","description":"why the prompt is invalid"}},"required":["message"]}}}],"add_generation_prompt":false}
+    """.strip().split(
+        "\n"
+    )
+    rows = [json.loads(row) for row in jsons]
+    return Dataset.from_list(rows)
+
+
+@pytest.fixture(name="qwen3_tokenizer")
+def qwen3_tokenizer_fixture(
+    download_qwen3_half_billion_model,
+):  # pylint: disable=unused-argument
+    tokenizer = AutoTokenizer.from_pretrained("Qwen/Qwen3-0.6B")
+
+    return tokenizer
+
+
+@pytest.fixture(name="qwen3_prompt_strategy")
+def qwen3_chat_template_strategy(qwen3_tokenizer):
+    cfg = DictDefault(
+        sequence_len=2048,
+        chat_template="qwen3",
+        eot_tokens=["<|im_end|>"],
+    )
+    ds_cfg = DictDefault(
+        type="chat_template",
+    )
+    load = StrategyLoader()
+    strat = load(qwen3_tokenizer, cfg, ds_cfg)
+    return strat
+
+
+class TestSchemaUnification:
+    """
+    Test class on handling null fields for tool calling
+    """
+
+    def test_schema_unification_single_prompt(
+        self, messages_w_tools, qwen3_prompt_strategy, qwen3_tokenizer
+    ):
+        for row in messages_w_tools:
+            inputs = qwen3_prompt_strategy.tokenize_prompt(row)
+            decoded = qwen3_tokenizer.decode(inputs["input_ids"])
+            tool_call = decoded.split("<tool_call>")[-1].split("</tool_call>")[0]
+            assert '"message": null' not in tool_call
+            assert '"theta": null' not in tool_call
+
+    def test_schema_unification_batched(
+        self, messages_w_tools, qwen3_prompt_strategy, qwen3_tokenizer
+    ):
+        rows = messages_w_tools.map(qwen3_prompt_strategy.tokenize_prompt, batched=True)
+        for row in rows:
+            decoded = qwen3_tokenizer.decode(row["input_ids"])
+            tool_call = decoded.split("<tool_call>")[-1].split("</tool_call>")[0]
+            assert '"message": null' not in tool_call
+            assert '"theta": null' not in tool_call