This book constitutes revised selected papers from the 13th International Workshop on Engineering Multi-Agent Systems, EMAS 2025, which took place in Detroit, USA, during May 19–20, 2025. The 13 full papers in this book were carefully reviewed and selected from a total of 16 submissions. The book also contains one paper on the community roadmap for EMAS. The contributions focus on topics such as agent-oriented software engineering, programming multi-agent systems, declarative agent languages and technologies, artificial intelligence, and machine learning.