In this paper we deal with the numerical analysis of an upscaled model of a reactive flow in a porous medium, which describes the transport of solutes undergoing precipitation and dissolution, leading to the formation/degradation of crystals inside the porous matrix. The model is defined at the Darcy scale, and it is coupled to a Darcy flow characterized by a permeability field that changes in space and time according to the precipitated crystal concentration. The model involves a non-linear multi-valued reaction term, which is treated exactly by solving an inclusion problem for the solutes and the crystals dynamics. We consider a weak formulation for the coupled system of equations expressed in a dual mixed form for the Darcy field and in ...