This paper proposes a digital model predictive controller (DMPC) for a multi-input multi-output (MIMO) DC-DC converter interfaced with renewable energy resources in a hybrid system. Such MIMO systems generally suffer from cross-regulation, which seriously impacts the stability and speed of response of the system. To solve the contemporary issues in a MIMO system, a controller is required to attenuate the cross-regulation. Therefore, this paper proposes a controller, which increases speed of response and maintains stable output by regulating the load voltage independently. The inductor current and the capacitor voltage of the proposed converter are considered as the controlling parameters. With the aid of Forward Euler’s procedure, the future values are computed for the instantaneous values of controlling parameters. Cost function defines the control action by the predicted values that describe the system performance and establish optimal condition at which the output of the system is required. This allows proper switching of the system, thereby helping to regulate the output voltages. Thus, for any variation in load, the DMPC ensures steady switching operation and minimization of cross-regulation. To prove the efficacy of proposed DMPC controller, simulations followed by the experimental results are executed on a hybrid system consisting of dual-input dual-output (DIDO) positive Super-Lift Luo converter (PSLLC) interfaced with photovoltaic renewable energy resource. The results thus obtained are compared with the conventional PID (proportional integrative derivative) controller for validation and prove that the DMPC controller is able to control the cross-regulation effectively.