This book constitutes the refereed proceedings of the 39th IFIP WG 11.3 Annual Conference on Data and Applications Security and Privacy XXXIX, DBSec 2025, held in Gjøvik, Norway, during June 23-24, 2025. The 19 full papers and 5 short papers included in this book were carefully reviewed and selected from 59 submissions. They were organized in topical sections as follows: AI applications in security and privacy; User and data privacy; Database and storage security; Differential privacy; Attackers and attack detection; Access control & Internal Controls and Audit process; and Cryptography for security and privacy.