Context. The primary objective of this article is to explore aspects related to ensuring security and enhancing the efficiency of authentication processes in intelligent systems through the application of visual biometrics. The focus is on advancing and refining authentication systems by employing sophisticated biometric identification methods. Objective. A specialized intelligent system has been developed, utilizing a Siamese neural network to establish secure user authentication within the existing system. Beyond incorporating fundamental security measures such as hashing and secure storage of user credentials, the contemporary significance of implementing two-factor authentication is underscored. This approach significantly fortifies user data protection, thwarting most contemporary hacking methods and safeguarding against data breaches. The study acknowledges certain limitations in its approach, possibly affecting the generalizability of the findings. These limitations provide avenues for future research and exploration, contributing to the ongoing evolution of authentication methodologies in intelligent systems. Method. The two-factor authentication system integrates facial recognition technology, employing visual biometrics for heightened security compared to alternative two-factor authentication methods. Various implementations of the Siamese neural network, utilizing Contrastive loss function and Triplet loss function, were evaluated. Subsequently, a neural network employing the Triplet loss function was implemented and trained. Results. The article emphasizes the practical implications of the developed intelligent system, showcasing its effectiveness in minimizing the risk of unauthorized access to user accounts. The integration of contemporary authentication methodologies ensures a secure and robust user authentication process. Conclusions. The implementation of facial recognition technology in authentication processes has broader social implications. It contributes to a more secure digital environment by preventing unauthorized access, ultimately safeguarding user privacy and data. The study’s originality lies in its innovative approach to authentication, utilizing visual biometrics within a Siamese neural network framework. The developed intelligent system represents a valuable contribution to the field, offering an effective and contemporary solution to user authentication challenges.