IoT-based multi-biometric system is a blend of multiple biometric templates that can be used for user authentication/verification using sensors. The leakage of the biometric trait information may cause critical privacy and security issues. It is expected to protect the privacy details of individuals through the irreversibility, unlinkability, and renewability of multi-biometric templates used in the authentication system. This study presents a robust authentication system with secure multi-biometric template protection techniques based on discrete cosine transform feature transformation and Lagrange’s interpolation-based image transformation. Three biometric traits namely iris, fingerprint, and palm print are recorded using sensors to validate the proposed multi-biometric template protection system. The fusion of all traits used is giving an average of 95.42% genuine acceptance rate and an average of 4.57% false rejection rate. Despite any number of biometric templates used for authentication, the proposed image transformation techniques keep the size of the final storage requirement as 8 X 8, which achieves constant space complexity (O(1)). The stored template is not linked with original templates; it is irreversible and renewable as new enrolment of the same individual will produce a new template every time. Overall, the proposed technique provides a secure authentication system with high accuracy, a constant size database, and the privacy preservation of biometric traits.