Hydrates and clathrates have been suggested as potential gas separation and storage materials. For the case of hydrogen, previous results have evidenced that hydroquinone clathrates represent a feasible alternative for storage if compared to other options. The possibility of multiple clathrate cell occupation has been already demonstrated, so the key for a practical implementation of this solution is a detailed knowledge about the clathrate filling mechanism, and the upper occupancy limits. Identifying the optimal conditions required to enhance structure occupation, and the atomic scale nature of the inclusion process itself, leads to the possibility of increasing hydrogen volumetric storage capacity. In this study, the hydroquinone clathrate hydrogen filling process has been analyzed through atomistic Grand-Canonical Monte Carlo (GCMC) molecular simulations over a wide temperature and pressure range. The results obtained describe quantitatively the theoretical clathrate filling process, as well as the succession of multiple occupancy modes for the crystalline clathrate cells. The isotherms obtained have been correlated accurately using a mathematical model derived from the classical equation of Langmuir isotherms. The molecular simulation results presented describe the maximum hydrogen structural capacity, providing a valuable insight on the occurrence of multiple occupancy modes, a phenomenon not well described yet. The methodology used in this case can be extended to analyze hydrogen storage capacity inside other nanoporous materials.