In microgrids, the use of fuel cells (FCs) supplied with hydrogen as a type of clean energy is continuously rising. Integrating FCs into microgrids has shown interesting advantages in improving the performance of microgrids and promoting the use of hydrogen energy. They are usually associated with other sources of energy, mostly intermittent, to feed a DC bus. However, FCs are current intensive sources that produce electricity at low voltage. DC-DC converters are used to adapt the FC voltage to the DC bus level. The suitable converter topology and the selected controller are also requested in most applications with stable output voltage and power quality. In this paper, nonlinear disturbance observer (NDOB)-based sliding mode control is proposed to the interleaved boost converter (IBC) to enhance the output robustness and weaken the influences brought by uncertainties in the input voltage and the load resistance. Rigorous stable analysis of NDOBs and global systems are presented and proved by Lyapunov functions. Last, the simulations were performed to verify the effectiveness of the proposed controller in light of the varying load resistance and input voltage.