Fuel Cells (FCs) have emerged as an important alternative to traditional power sources due to their efficiency, reliability, high-power density, and clean energy. Given these attributes, FCs can enhance the performance of multi-energy systems involving intermittent renewable energy sources, providing stable power output when other renewable sources are not available. However, the integration of these electrochemical devices into hybrid systems presents several challenges that need to be addressed. Particularly, in scenarios where the system must deal with variable power demand, fuel cells alone may not effectively respond to abrupt fluctuations. So, FCs must be integrated with an energy storage system, involving supercapacitors or lithium batteries, to assist in handling peak load demands. This configuration gives rise to various multi-energy topologies, where the control system schemes play a crucial role. In this context, Sliding Mode Control (SMC) has proven to be a robust technique for nonlinear systems, particularly suitable for power systems involving fuel cells. Therefore, this chapter addresses the application of advanced SMC techniques to fuel cell-based hybrid energy systems. The design and implementation of SMC for different types of multi energy systems are discussed, including those incorporating batteries, supercapacitors, and renewable energy sources. The effectiveness of the attained controllers is demonstrated through validation tests, which show improved performance and stability compared to traditional control methods.