# Beyond the Protocol: Unveiling Attack Vectors in the Model Context Protocol (MCP) Ecosystem

arXiv: https://arxiv.org/abs/2506.02040 · HTML: https://mlsanity.com/paper/2506.02040/

## Key facts

- Cited by 19 papers in the map (data through 14 Oct 2026).
- Placed in Agent threats, guardrails and governance, one of 16 directions in LLM agents and tool use.
- Builds on 25 of its 70 references that are in the map.
- First posted on arXiv 31 May 2025.

## Placed in

- LLM agents and tool use / [Agent threats, guardrails and governance](https://mlsanity.com/agents/agent-threats-guardrails-and-governance/)

## Builds on (most cited first, 25 of 25)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Not what you've signed up for: Compromising Real-World LLM-Integrated Applications with Indirect Prompt Injection](https://mlsanity.com/paper/2302.12173/) (2023)
- [A Survey on Evaluation of Large Language Models](https://mlsanity.com/paper/2307.03109/) (2023)
- [Chatbot Arena: An Open Platform for Evaluating LLMs by Human Preference](https://mlsanity.com/paper/2403.04132/) (2024)
- [Prompt Injection attack against LLM-integrated Applications](https://mlsanity.com/paper/2306.05499/) (2023)
- [API-Bank: A Comprehensive Benchmark for Tool-Augmented LLMs](https://mlsanity.com/paper/2304.08244/) (2023)
- [Agent Security Bench (ASB): Formalizing and Benchmarking Attacks and Defenses in LLM-based Agents](https://mlsanity.com/paper/2410.02644/) (2024)
- [Model Context Protocol (MCP): Landscape, Security Threats, and Future Research Directions](https://mlsanity.com/paper/2503.23278/) (2025)
- [Benchmarking and Defending Against Indirect Prompt Injection Attacks on Large Language Models](https://mlsanity.com/paper/2312.14197/) (2023)
- [WASP: Benchmarking Web Agent Security Against Prompt Injection Attacks](https://mlsanity.com/paper/2504.18575/) (2025)
- [Optimization-based Prompt Injection Attack to LLM-as-a-Judge](https://mlsanity.com/paper/2403.17710/) (2024)
- [DataSentinel: A Game-Theoretic Detection of Prompt Injection Attacks](https://mlsanity.com/paper/2504.11358/) (2025)
- [AI Agents Under Threat: A Survey of Key Security Challenges and Future Pathways](https://mlsanity.com/paper/2406.02630/) (2024)
- [A Comprehensive Survey in LLM(-Agent) Full Stack Safety: Data, Training and Deployment](https://mlsanity.com/paper/2504.15585/) (2025)
- [A Review of Prominent Paradigms for LLM-Based Agents: Tool Use (Including RAG), Planning, and Feedback Learning](https://mlsanity.com/paper/2406.05804/) (2024)
- [Enterprise-Grade Security for the Model Context Protocol (MCP): Frameworks and Mitigation Strategies](https://mlsanity.com/paper/2504.08623/) (2025)
- [Securing Large Language Models: Threats, Vulnerabilities and Responsible Practices](https://mlsanity.com/paper/2403.12503/) (2024)
- [RMCBench: Benchmarking Large Language Models' Resistance to Malicious Code](https://mlsanity.com/paper/2409.15154/) (2024)
- [MCP Guardian: A Security-First Layer for Safeguarding MCP-Based AI System](https://mlsanity.com/paper/2504.12757/) (2025)
- [CheatAgent: Attacking LLM-Empowered Recommender Systems via LLM Agent](https://mlsanity.com/paper/2504.13192/) (2025)
- [BDMMT: Backdoor Sample Detection for Language Models through Model Mutation Testing](https://mlsanity.com/paper/2301.10412/) (2023)
- [Attacks on Third-Party APIs of Large Language Models](https://mlsanity.com/paper/2404.16891/) (2024)
- [Defense against Prompt Injection Attacks via Mixture of Encodings](https://mlsanity.com/paper/2504.07467/) (2025)
- [Governance of Generative AI in Creative Work: Consent, Credit, Compensation, and Beyond](https://mlsanity.com/paper/2501.11457/) (2025)
- [Smart Contract Security: a Practitioners' Perspective](https://mlsanity.com/paper/2102.10963/) (2021)

## Built on by (most cited first, 19 of 19)

- [AgentBound: Securing Execution Boundaries of AI Agents](https://mlsanity.com/paper/2510.21236/) (2025)
- [Security Threat Modeling for Emerging AI-Agent Protocols: A Comparative Analysis of MCP, A2A, Agora, and ANP](https://mlsanity.com/paper/2602.11327/) (2026)
- [MindGuard: Intrinsic Decision Inspection for Securing LLM Agents Against Metadata Poisoning](https://mlsanity.com/paper/2508.20412/) (2025)
- [Model Context Protocol Threat Modeling and Analyzing Vulnerabilities to Prompt Injection with Tool Poisoning](https://mlsanity.com/paper/2603.22489/) (2026)
- [Detecting Malicious Agent Skills in the Wild using Attention](https://mlsanity.com/paper/2606.23416/) (2026)
- [Toward Secure LLM Agents: Threat Surfaces, Attacks, Defenses, and Evaluation](https://mlsanity.com/paper/2606.10749/) (2026)
- [MCP-38: A Comprehensive Threat Taxonomy for Model Context Protocol Systems (v1.0)](https://mlsanity.com/paper/2603.18063/) (2026)
- [Human oversight of agentic systems in practice: Examining the oversight work, challenges, and heuristics of developers using software agents](https://mlsanity.com/paper/2606.05391/) (2026)
- [Help or Hurdle? Rethinking Model Context Protocol-Augmented Large Language Models](https://mlsanity.com/paper/2508.12566/) (2025)
- [When Agents Overtrust Environmental Evidence: An Extensible Agentic Framework for Benchmarking Evidence-Grounding Defects in LLM Agents](https://mlsanity.com/paper/2605.08828/) (2026)
- [When Child Inherits: Modeling and Exploiting Subagent Spawn in Multi-Agent Networks](https://mlsanity.com/paper/2605.08460/) (2026)
- [Securing the AI Agent: A Unified Framework for Multi-Layer Agent Red Teaming](https://mlsanity.com/paper/2606.31227/) (2026)
- [Can LLM Infer Risk Information From MCP Server System Logs?](https://mlsanity.com/paper/2511.05867/) (2025)
- [VIPER-MCP: Detecting and Exploiting Taint-Style Vulnerabilities in Model Context Protocol Servers](https://mlsanity.com/paper/2605.21392/) (2026)
- [Unicode TAG-Block Concealment of Tool-Metadata Payloads in the Model Context Protocol: An Approval-View Fidelity Gap Across Three Independent Server Implementations](https://mlsanity.com/paper/2607.05744/) (2026)
- [ECLIPSE: Self-Evolving Stealthy Prompt Injection Attack against Long-Horizon Agentic Systems](https://mlsanity.com/paper/2608.30441/) (2026)
- [When the Agent Becomes the Kernel: A Systematization of Security on the Path to AI-Native Operating Systems](https://mlsanity.com/paper/2609.23700/) (2026)
- [A2M: Trace-Optimized Agent Hijacking in the MCP Ecosystem](https://mlsanity.com/paper/2609.26761/) (2026)
- [APEX: Active Protection at Execution Boundaries for LLM Agents](https://mlsanity.com/paper/2610.06966/) (2026)

## Abstract (arXiv)

The Model Context Protocol (MCP) is an emerging standard designed to enable seamless interaction between Large Language Model (LLM) applications and external tools or resources. Within a short period, thousands of MCP services have been developed and deployed. However, the client-server integration architecture inherent in MCP may expand the attack surface against LLM Agent systems, introducing new vulnerabilities that allow attackers to exploit by designing malicious MCP servers. In this paper, we present the first end-to-end empirical evaluation of attack vectors targeting the MCP ecosystem. We identify four categories of attacks, i.e., Tool Poisoning Attacks, Puppet Attacks, Rug Pull Attacks, and Exploitation via Malicious External Resources. To evaluate their feasibility, we conduct experiments following the typical steps of launching an attack through malicious MCP servers: upload -> download -> attack. Specifically, we first construct malicious MCP servers and successfully upload them to three widely used MCP aggregation platforms. The results indicate that current audit mechanisms are insufficient to identify and prevent these threats. Next, through a user study and interview with 20 participants, we demonstrate that users struggle to identify malicious MCP servers and often unknowingly install them from aggregator platforms. Finally, we empirically demonstrate that these attacks can trigger harmful actions within the user's local environment, such as accessing private files or controlling devices to transfer digital assets. Additionally, based on interview results, we discuss four key challenges faced by the current MCP security ecosystem. These findings underscore the urgent need for robust security mechanisms to defend against malicious MCP servers and ensure the safe deployment of increasingly autonomous LLM agents.