DC microgrid applications include electric vehicle systems, shipboard power systems, and More Electric Aircraft (MEA), which produce power at a low voltage level. Rapid developments in hydrogen fuel cell (FC) energy have extended the applications of multi-phase parallel interleaved step-up converters in stabilizing DC bus voltage. The cascade architecture of power converters in DC microgrids may lead to large oscillation and even risks of instability given that the load converters considered as loads feature constant power load (CPL) characteristics. In this article, the output DC bus voltage stabilization and the current sharing of a multi-phase parallel interleaved FC boost converter is presented. The extended Port-Hamiltonian (pH) form has been proposed with the robust controller by adding an integrator action based on the Lyapunov−Energy function, named “Adaptive Hamiltonian PI controller”. The stability and robustness of the designed controller have been estimated by using Mathematica and Matlab/Simulink environments and successfully authenticated by performing experimental results in the laboratory. The results have been obtained using a 2.5 kW prototype FC converter (by two-phase parallel interleaved boost converters) with a dSPACE MicroLabBox platform. The FC main source system is based on a fuel reformer engine that transforms fuel methanol and water into hydrogen gas H2 to a polymer electrolyte membrane FC stack (50 V, 2.5 kW).