Deep geological disposal is the preferred solution for radioactive waste management in many countries, including Belgium, where the Boom Clay is one of the potential candidate host formations. Over the long term, corrosion mechanisms are expected to release large amounts of gas that will rise in pressure and activate different gas transport processes in the system and the surrounding geological formation. Assessing which transfer mode prevails under which range of pressure conditions in the sound rock layers remains a major issue. This paper presents a multi-scale Hydro-Mechanical (HM) model capturing the influence of the microstructure features on the macroscopic gas flow, and especially the emergence of preferential gas-filled pathways. A detailed constitutive model for partially saturated clay materials is developed from experimental data to perform the modelling of a Representative Element Volume (REV), and integrated into a multi-scale scheme using homogenisation and localisation techniques for the transitions to the macroscopic scale. Using this tool, numerical modelling of a gas injection test in the Boom Clay is performed with the aim of improving the mechanistic understanding of gas transport processes in natural clay barriers.