Prompt optimization can improve multi-agent LLM systems, but the prompts being optimized often serve two entangled roles: generating task-relevant content and specifying execution-critical protocols, such as message routing, output formatting, and termination signals, on which the underlying code relies. As a result, a prompt edit intended to improve content generation can inadvertently corrupt the protocol and cause the entire agent pipeline to fail. Our key observation is that these two roles have different representations: execution protocols are typically structured, while task-relevant content is usually expressed in unstructured language. Based on this, we propose control-data flow separation, where execution-critical control is represented as typed, validated program objects, while task-relevant language remains the optimizable data flow for agent communication. This design allows optimizers to improve multi-agent behavior without exposing the routing or formatting interface to prompt drift. Across synthetic reasoning, collaborative review generation, and insurance rating workflows, our framework empirically achieves 100% eventual protocol validity while consistently improving task performance.
Large language model (LLM)-based Multi-agent systems (MAS) have shown promise in tackling complex collaborative tasks, where agents are typically orchestrated via role-specific prompts. While the quality of these prompts is pivotal, jointly optimizing them across interacting agents remains a non-trivial challenge, primarily due to the misalignment between local agent objectives and holistic system goals. To address this, we introduce MASPO, a novel framework designed to automatically and iteratively refine prompts across the entire system. A core innovation of MASPO is its joint evaluation mechanism, which assesses prompts not merely by their local validity, but by their capacity to facilitate downstream success for successor agents. This effectively bridges the gap between local interactions and global outcomes without relying on ground-truth labels. Furthermore, MASPO employs a data-driven evolutionary beam search to efficiently navigate the high-dimensional prompt space. Extensive empirical evaluations across 6 diverse tasks demonstrate that MASPO consistently outperforms state-of-the-art prompt optimization methods, achieving an average accuracy improvement of 2.9. We release our code at https://github.com/wangzx1219/MASPO.
Multi-agent systems (MAS) offer a scalable path forward for agentic AI, comprising multiple LLM-based agents, each assigned a system prompt and a position within a workflow that governs inter-agent coordination and output aggregation. System prompts thus form a critical and accessible optimization surface: they specify agents' roles and behaviors, enabling system-level improvements without model finetuning. Although prompt optimization has shown substantial potential for single LLMs, extending it to MAS poses distinct challenges, notably an exponentially growing search space. It remains unclear whether, when, and by how much prompt optimization improves MAS performance, and how sensitive such gains are to system configuration. In this work, we systematically study system-prompt optimization across a broad range of MAS setups varying in task, workflow, communication protocol, and team size, benchmarking two prompt optimizers that naturally extend state-of-the-art single-agent methods. The results reveal its potential to unlock significant gains while exposing open challenges, characterizing when and how much prompt optimization helps across diverse MAS settings.
LLM agents in interactive environments are highly sensitive to their prompts, yet prompt engineering remains a manual, task-specific process. We introduce an automated prompt optimization framework for LLM agents that decomposes the observation-to-action pipeline into a goal-conditioned descriptor agent and an action selection agent, and iteratively refines each module's prompt through an LLM-driven evolutionary loop guided by environment returns. We propose a behavior analyzer to attribute episode outcomes to specific prompt components, and a mutator to propose targeted revisions to the prompt, before validating them through environment rollouts. We evaluate on all five BabyAI tasks in the BALROG benchmark, comparing our pipeline against BALROG's RobustCoTAgent under both plain and guided prompt initializations. Optimization improves performance consistently across tasks and conditions, without requiring updates to the model weights. On PutNext, a multi-step coordination task where the RobustCoTAgent achieves 0% success, our framework reaches up to 72.5% success rate using the same underlying LLM with optimized prompts. These results suggest that a multi-agent framework, combined with automatic prompt optimization, enhances LLMs without the need for fine-tuning or extensive human supervision.