Multi-biometric systems have been widely accepted in various applications due to its capability to solve the limitations of unimodal systems. Directly storing the biometric templates into a centralised server leads to privacy concerns. In the past few years, many biometric authentication systems based on homomorphic encryption have been introduced to provide security for the templates. Most of the existing solutions rely on an implication of the assumption that the server is ‘honest-but-curious’. Therefore, the compromise of server results into the entire system vulnerability and fails to provide the integrity. To address this, we propose a novel multi-instance iris authentication system, BMIAE to deal with malicious attacks over the transmission channel and at the untrusted server. BMIAE encrypt the iris templates using ElGamal encryption to guarantee confidentiality and Smart contract running on a Blockchain helps to achieve the integrity of templates and matching result. BMIAE also addresses the limitations of using Blockchain for biometrics like privacy and expensive storage. To check the effectiveness and robustness, BMIAE has experimented on CASIA-V3-Interval, IITD and SDUMLA-HMT iris databases. Experimental results show that BMIAE provides improved accuracy, and eliminates the need to trust the centralised server when compared to the state-of-the-art approaches.