Nowadays, standalone microgrids that make use of renewable energy sources have gained great interest. They provide a viable solution for rural electrification and decrease the burden on the utility grid. However, because standalone microgrids are nonlinear and time-varying, controlling and managing their energy can be difficult. A fractional-order proportional integral (FOPI) controller was proposed in this study to enhance a standalone microgrid’s energy management and performance. An ultra-capacitor (UC) and a battery, called a hybrid energy storage scheme, were employed as the microgrid’s energy storage system. The microgrid was primarily powered by solar and wind power. To achieve optimal performance, the FOPI’s parameters were ideally generated using the gorilla troop optimization (GTO) technique. The FOPI controller’s performance was contrasted with a conventional PI controller in terms of variations in load power, wind speed, and solar insolation. The microgrid was modeled and simulated using MATLAB/Simulink software R2023a 23.1. The results indicate that, in comparison to the traditional PI controller, the proposed FOPI controller significantly improved the microgrid’s transient performance. The load voltage and frequency were maintained constant against the least amount of disturbance despite variations in wind speed, photovoltaic intensity, and load power. In contrast, the storage battery precisely stores and releases energy to counteract variations in wind and photovoltaic power. The outcomes validate that in the presence of the UC, the microgrid performance is improved. However, the improvement is very close to that gained when using the proposed controller without UC. Hence, the proposed controller can reduce the cost, weight, and space of the system. Moreover, a Hardware-in-the-Loop (HIL) emulator was implemented using a C2000™ microcontroller LaunchPad™ TMS320F28379D kit (Texas Instruments, Dallas, TX, USA) to evaluate the proposed system and validate the simulation results.