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.