This paper focuses on the real-time implementation of an optimal high-performance control applied to an interleaved nonisolated DC/DC converter designed for fuel cell applications. Three-phase interleaved boost converters are utilized to minimize input current undulation, increase efficiency, and provide a high output voltage in order to ensure the performance of the FC stack. The proposed control strategy contains an outer loop that generates the reference current based on a two-degree-of-freedom PID controller. This controller provides a robust setpoint tracking and disturbance rejection, which improves the system’s response and efficiency. A fast inner regulation loop based on a super-twisting integral sliding mode (STISM) algorithm is developed to achieve a fixed converter output voltage, equitable phase current sharing, and fast regulation against load disturbances in failure operation. The STISM algorithm exhibits a rapid convergence property of the sliding mode and effectively avoids the chattering phenomena frequently observed in conventional sliding modes. The proposed controller’s gains are determined using the atom search optimization algorithm, which ensures exceptional reliability and a high degree of robustness and stability of the controllers under a variety of operational conditions. This method is inspired from the behavior of atoms and their electrons during the excitation process leading to a one-of-a-kind optimization technique which contributes to the controller’s reliability. Using Matlab-Simulink simulation tools, the efficacy and performance of the designed control have first been evaluated and assessed and compared with other optimization algorithms, and then with a dual loop based on a PID controller. Then, they have been verified by real-time hardware implementation on a 1.2 KW prototype FC converter driven by the dSPACE-1104 card under a variety of tests. The suggested approach offers impressive experimental results in dynamic and steady states.