Smart cities and their applications have become attractive research fields birthing numerous technologies. Fifth generation (5G) networks are important components of smart cities, where intelligent access control is deployed for identity authentication, online banking, and cyber security. To assure secure transactions and to protect user’s identities against cybersecurity threats, strong authentication techniques should be used. The prevalence of biometrics, such as fingerprints, in authentication and identification makes the need to safeguard them important across different areas of smart applications. Our study presents a system to detect alterations to biometric modalities to discriminate pristine, adulterated, and fake biometrics in 5G-based smart cities. Specifically, we use deep learning models based on convolutional neural networks (CNN) and a hybrid model that combines CNN with convolutional long-short term memory (ConvLSTM) to compute a three-tier probability that a biometric has been tempered. Simulation-based experiments indicate that the alteration detection accuracy matches those recorded in advanced methods with superior performance in terms of detecting central rotation alteration to fingerprints. This makes the proposed system a veritable solution for different biometric authentication applications in secure smart cities.