This book constitutes the refereed proceedings of the 12th International Conference on Future Data and Security Engineering, FDSE 2025, held in Ho Chi Minh City, Vietnam, during November 27–29, 2025.The 56 full papers and 10 short papers presented in these two volumes were carefully reviewed and selected from 215 submissions. The papers are organized in the following topical sections: Part I: Invited Keynote; Advances in Machine Learning for Big Data Analytics; Security and Privacy Engineering; Query Processing and Optimization; Data Analytics and Healthcare Systems; Smart City and Industry 4.0 Applications. Part II: Invited Keynote; Advances in Machine Learning for Big Data Analytics; Security and Privacy Engineering; Query Processing and Optimization; Data Analytics and Healthcare Systems; Smart City and Industry 4.0 Applications; Short Papers: Security and Data Engineering.