We develop a framework for multibiometric systems, which combines a deep learning technique with the serial fusion method. Deep learning techniques have been used in unimodal and parallel fusion-based multimodal biometric systems in the past few years. While deep learning techniques have been successful in improving the authentication accuracy, a biometric system is still challenged by two issues: 1) a unimodal system suffers from environmental interference, spoofing attacks, and nonuniversality, and 2) a parallel fusion-based multimodal system suffers from user inconvenience as it requires the user to provide multiple biometrics, which in turn takes longer verification times. A serial fusion method can improve user convenience in a multibiometric system by requiring a user to submit only a subset of the available biometrics. To our knowledge, the effectiveness of using a deep learning technique with a serial fusion method in multibiometric systems is still underexplored. In this article, we close this research gap. We develop a three-stage multibiometric system using a user's fingerprint, palm, and face and test three serial fusion methods with a Siamese neural network. Our experiments achieve an AUC of 0.9996, where the genuine users require only 1.56 biometrics (instead of all 3) on an average. Impact statement-We work on enhancing the user convenience and reducing the verification error in a multibiometric system. An improved multibiometric system can help law enforcement, homeland security, defense, and our daily lives by providing better access control. With the advent of deep learning technologies, the accuracy of multibiometric systems have been improved significantly; however, its applicability is still in question because of long verification times required by parallel fusion in a multibiometric system. Our proposed multibiometric framework alleviates this user inconvenience issue by utilizing a serial fusion strategy in decision making and improves accuracy by leveraging deep learning technology in feature extraction and score generation. © 2020 IEEE.