Biometrics security is a dynamic research area spurred by the need to protect personal traits from threats like theft, non-authorised distribution, reuse and so on. A widely investigated solution to such threats consists of processing the biometric signals under encryption, in order to avoid any leakage of information towards non-authorised parties. In this study, the authors propose to leverage on the superior performance of multimodal biometric recognition to improve the efficiency of a biometric-based authentication protocol operating on encrypted data under the malicious security model. In the proposed protocol, authentication relies on both facial and iris biometrics, whose representation accuracy is specifically tailored to the trade-off between recognition accuracy and efficiency. From a cryptographic point of view, the protocol relies on Damgård et al. SPDZ. Experimental results show that the multimodal protocol is faster than corresponding unimodal protocols achieving the same accuracy.