This paper proposes a robust controller for the generation of stable limit cycles in multi-input mechanical systems subjected to model uncertainties. The proposed idea is based on Port-Controlled Hamiltonian (PCH) model and energy-based control by considering the Hamiltonian function as the Lyapunov function. For this purpose, first, a nominal controller is designed by shaping the energy function of the system according to the structure of the desired limit cycle. Then, an additional robustifying control term is designed based on the integral sliding mode method with the selection of an appropriate sliding surface. Finally, computer simulations for two practical case studies are provided to confirm the effectiveness of the proposed controller in the generation of stable limit cycles in the presence of uncertainties.