The study proposed and designed a cloud-native security architecture that improved data protection of private academic institutions’ information systems in Uganda with Valley University of Science and Technology (VUST), Bushenyi serving as a case study. The study was guided by four objectives; i) Determining data protection strategies implemented at VUST learning information systems. ii) Finding out how well cloud-native security technology was utilised to improve threat detection/response and data integrity at VUST. iii) Determining the relationship between cloud-native security architecture and data protection at VUST, iv) Proposing a cloud-native security architecture to improve data protection at VUST.