Model Predictive Control (MPC) has emerged as a promising alternative for controlling power converters, offering benefits such as flexibility, simplicity, and rapid control response, particularly when short-horizon algorithms are employed. This paper introduces a system using a short-horizon Finite Control Set MPC (FCS-MPC) strategy to specifically address the challenge of non-minimum phase behavior in boost converters. The non-minimum phase issue, which complicates the control process by introducing an initial inverse response, is effectively mitigated by the proposed method. A Proportional–Integral (PI) controller is integrated to dynamically adjust the reference current based on the output voltage error, thereby enhancing overall system stability and performance. Unlike conventional PI-MPC methods, where the PI controller has an influence on the system dynamics, the PI controller in this approach is solely used for tuning the reference current needed for the FCS-MPC controller. The PI controller addresses small deviations in output voltage, primarily due to model prediction inaccuracies, ensuring steady-state accuracy, while the FCS-MPC handles fast dynamic responses to adapt the controller’s behavior based on load conditions. This dual control strategy effectively balances the need for precise voltage regulation and rapid adaptation to varying load conditions. The proposed method’s effectiveness is validated through a multi-stage simulation test, demonstrating significant improvements in response time and stability compared to traditional control methods. Hardware-in-the-loop testing further confirms the system’s robustness and potential for real-time applications in power electronics.