diff --git a/api/core/workflow/nodes/agent/agent_node.py b/api/core/workflow/nodes/agent/agent_node.py
index 3aebd64160..5882ff7bcb 100644
--- a/api/core/workflow/nodes/agent/agent_node.py
+++ b/api/core/workflow/nodes/agent/agent_node.py
@@ -31,7 +31,7 @@ from core.tools.entities.tool_entities import (
     ToolProviderType,
 )
 from core.tools.tool_manager import ToolManager
-from core.variables.segments import ArrayFileSegment, FileSegment, StringSegment
+from core.variables.segments import ArrayFileSegment, FileSegment, StringSegment, ArrayAnySegment
 from core.workflow.entities.node_entities import NodeRunResult
 from core.workflow.entities.variable_pool import VariablePool
 from core.workflow.entities.workflow_node_execution import WorkflowNodeExecutionStatus
@@ -190,6 +190,27 @@ class AgentNode(ToolNode):
         """
         agent_parameters_dictionary = {parameter.name: parameter for parameter in agent_parameters}
 
+        # Determine once whether this node references sys.files anywhere and whether that variable is empty.
+        def _input_uses_sys_files(_agent_input):
+            if _agent_input.type == "variable":
+                return _agent_input.value == ["sys", SystemVariableKey.FILES.value]
+            if _agent_input.type in {"mixed", "constant"}:
+                return "sys.files" in str(_agent_input.value)
+            return False
+
+        uses_sys_files_for_node: bool = any(
+            _input_uses_sys_files(inp) for inp in node_data.agent_parameters.values()
+        )
+
+        sys_files_segment = variable_pool.get(["sys", SystemVariableKey.FILES.value])
+        sys_files_empty: bool = (
+            sys_files_segment is None
+            or (
+                isinstance(sys_files_segment, (ArrayFileSegment, ArrayAnySegment))
+                and len(sys_files_segment.value) == 0
+            )
+        )
+
         result: dict[str, Any] = {}
         for parameter_name in node_data.agent_parameters:
             parameter = agent_parameters_dictionary.get(parameter_name)
@@ -402,6 +423,10 @@ class AgentNode(ToolNode):
                                     pass
 
                             value["history_prompt_messages"] = history_prompt_messages
+            # If sys.files is empty, strip any leftover "[]" placeholder from strings (both log and runtime params).
+            if sys_files_empty and isinstance(value, str):
+                value = value.replace("[]", "").rstrip()
+
             result[parameter_name] = value
 
         return result