Storing methane in clathrates is one of the most promising alternatives for transporting natural gas (NG) as it offers similar gas densities as liquefied and compressed NG while offering lower safety risks. However, the practical use of clathrates is limited given the extremely low temperatures and high pressures necessary to form these structures. Therefore, it has been suggested to confine clathrates in nanoporous materials, as this can relent clathrate’s formation conditions while preserving its CH4 volumetric storage. Yet, the choice of nanoporous materials to be employed as clathrate growing platform is still rather arbitrary. Herein, we tackle this challenge in a systematic way by computationally exploring the stability of clathrates confined in alkyl-grafted silica materials with different pore sizes, ligand densities and ligand types. Based on our findings we are able to propose key design criteria for nanoporous materials favoring the stability of a neighbouring clathrate phase, namely large pore sizes, high ligand densities, and smooth pore walls. We hope the atomistic insight provided in this work will guide and facilitate the development of new nanomaterials designed to promote the formation of clathrates.