Suffusion, a particular case of internal erosion in soils, is a particle-scale mechanism involving the selective erosion of fine particles within the matrix of coarse particles under the effect of water seepage. Modifications in the micro-structure as a consequence of the loss of a fine fraction may affect both the hydraulic and the mechanical properties of the soil. Thus leading, in some cases, to drastic consequences. In this study, a discrete numerical model methodology is introduced to investigate the initiation and development of suffusion as well as to analyse its effects on the soil mechanical properties. For that purpose, an original numerical extraction procedure was developed allowing us to mimic the suffusion process by taking into account both the micro-structure of the granular packing and the hydraulic loading in the suffusion development. Such a procedure is based on a one-way fluid-solid coupling where the interstitial flow is solved with a finite volume approach defined at the pore scale. Numerical soil samples subjected to different hydraulic gradients show that depending on the amount and the role of eroded particles in the granular assembly, the eroded medium either shows negligible deformations during erosion but then collapses suddenly once sheared or it deforms significantly during erosion and recovers part of its strength once subjected to shear forces. A non-linear non-monotonic relation between the eroded mass and the mechanical properties of the soil was found.