We present a 3D model coupling a discrete element model and a pore network model specifically developed to describe the different diffusion mechanisms at stake in coal matrix as well as the associated adsorption induced deformations. The material is assumed to be saturated with gas and diffusion occurs through the combination of Knudsen diffusion within the pore space, surface diffusion at the solid surface, and adsorption–desorption at the pore-solid interface. The model is hydro-mechanically coupled in the sense that changes in pore pressure produce hydrostatic forces that deform the solid skeleton, while deformation of the pore space induces pore pressure changes that promote interpore flow. Sorption induced deformations are taken into account by considering an additional pressure term related to the concentration of gas within the medium (the so-called solvation pressure). The implemented transport models are verified against analytical solutions describing diffusion in porous media with and without sorption–desorption, and a comparison is made with a swelling experiment performed on a coal specimen to illustrate the relevance of the proposed approach for describing adsorption induced deformation. As a result, this new pore-scale model offers a precise way to assess coal matrix sorption induced deformation and contributes to the knowledge of CBM storage and transport processes.