Microgrids based on fuel cells are used to produce energy due to their zero emissions, stand-alone operation, and compact size that facilitates mobility; making research in fuel cell applications essential to support their widespread adoption. This paper proposes two main contributions: the adaptation of a TMDSSOLARUINVKIT microinverter for integration into a microgrid powered by a fuel cell, and the design and implementation of adaptive controllers. The controllers ensure the proper operation of the microgrid and avoid the fuel cell starvation. The microgrid comprises a fuel cell emulator, a TMDSSOLARUINVKIT microinverter, and AC linear and nonlinear loads. The research methodology follows three steps. First, a hardware-in-the-loop approach is proposed to emulate the fuel cell using a real-time target machine and a power interface, utilizing a model derived from the fuel cell manufacturer’s specifications. Then, a detailed model of a flyback converter is obtained to design and implement a control system, consisting of two adaptive controllers, one for regulating the current of the fuel cell and another for controlling the DC-link voltage. The current controller adapts a proportional gain to ensure a desired cut-off frequency and the DC-link voltage controller adapts a proportional and integral gains due changes in the duty cycle, ensuring the proper operation in any operating condition. Finally, the functionality of the microgrid based on a fuel cell is validated through four experiments. The results confirm the effective operation of the controllers ensuring the safe operation of the fuel cell. One experiment is designed to demonstrate the capability of the proposed solution to meet the requirements of rural areas in Colombia.