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With the booming integration of IoT technology in our daily life applications such as smart industrial, smart city, smart home, smart grid, and healthcare, it is essential to ensure the security and privacy challenges of these systems. Furthermore, time-critical IoT applications in healthcare require access from external parties (users) to their real-time private information via wireless communication devices. Therefore, challenges such as user authentication must be addressed in IoT wireless sensor networks (WSNs). In this paper, we propose a secure and lightweight three-factor (3FA) user authentication protocol based on feature extraction of user biometrics for future IoT WSN applications. The proposed protocol is based on the hash and XOR operations, including (i) a 3-factor authentication (i.e., smart device, biometrics, and user password); (ii) shared session key; (iii) mutual authentication; and (iv) key freshness. We demonstrate the proposed protocol’s security using the widely accepted Burrows–Abadi–Needham (BAN) logic, Automated Validation of Internet Security Protocols and Applications (AVISPA) simulation tool, and the informal security analysis that demonstrates its other features. In addition, our simulations prove that the proposed protocol is superior to the existing related authentication protocols, in terms of security and functionality features, along with communication and computation overheads. Moreover, the proposed protocol can be utilized efficiently in most of IoT’s WSN applications, such as wireless healthcare sensor networks.