diff --git a/src/backend/base/langflow/base/models/model.py b/src/backend/base/langflow/base/models/model.py
index 35853b2c2852..6a2aeda1d534 100644
--- a/src/backend/base/langflow/base/models/model.py
+++ b/src/backend/base/langflow/base/models/model.py
@@ -143,20 +143,24 @@ def get_chat_result(
         messages: list[Union[BaseMessage]] = []
         if not input_value and not system_message:
             raise ValueError("The message you want to send to the model is empty.")
-        if system_message:
-            messages.append(SystemMessage(content=system_message))
+        system_message_added = False
         if input_value:
             if isinstance(input_value, Message):
                 with warnings.catch_warnings():
                     warnings.simplefilter("ignore")
                     if "prompt" in input_value:
                         prompt = input_value.load_lc_prompt()
+                        if system_message:
+                            prompt.messages = [SystemMessage(content=system_message)] + prompt.messages
+                            system_message_added = True
                         runnable = prompt | runnable
                     else:
                         messages.append(input_value.to_lc_message())
             else:
                 messages.append(HumanMessage(content=input_value))
 
+        if system_message and not system_message_added:
+            messages.append(SystemMessage(content=system_message))
         inputs: Union[list, dict] = messages or {}
         try:
             runnable = runnable.with_config(  # type: ignore