Particles slide and roll on each other when a granular medium is sheared. Consequently, the tribological properties, such as inter-particle friction and adhesion, play a major role in influencing their bulk failure and rheology. Although the influence of roughness on adhesion and friction of contacting surfaces is known, the incorporation of the surface roughness in the numerical modelling of granular materials has received little attention. In this study, the boundary element method (BEM), which is widely used for simulating the mechanics of interacting surfaces, is coupled with discrete element method (DEM) and the bulk deformation of granular materials is analysed. A BEM code, developed in-house, is employed to calculate the normal force-displacement behaviour for rough contact deformations, based on which a contact model is proposed. This is an efficient and relatively fast method of calculating the contact mechanics of rough surfaces. The resulting model is then implemented in the simulations by DEM to determine the effect of micro-scale surface roughness on the bulk compression of granular materials. This study highlights the importance of the effect of surface characteristics on contact behaviour of particles for the case of shallow footing and provides an efficient approach for modelling the flow behaviour of a large number of rough particles. Keywords Contact mechanics • Numerical modelling • Discrete element method • Boundary element method List of symbols A c Area of contact E Elastic modulus E * Effective contact elastic modulus H Hardness N Total number of nodes in the domain φ Coefficient of friction p s 1 , s 2 Applied contact pressure r Rigid body movement of two rough surfaces in normal direction R Radius of sphere s 1 , s 2 Coordinate of area that pressure is applied S q Root mean squared height u z (x,y) Material deformation F N Load in the normal direction (x, y) Coordinate in which surface deformation is obtained Z 1 , Z 2 The surface profiles of the two rough particles α, β Roughness parameters ν Poisson's ratio