Mineral precipitation and dissolution processes in a porous medium can alter the structure of the medium at the scale of pores. Such changes make numerical simulations a challenging task as the geometry of the pores changes in time in an apriori unknown manner. To deal with such aspects, we here adopt a two-scale phase-field model, and propose a robust scheme for the numerical approximation of the solution. The scheme takes into account both the scale separation in the model, as well as the non-linear character of the model. After proving the convergence of the scheme, an adaptive two-scale strategy is incorporated, which improves the efficiency of the simulations. Numerical tests are presented, showing the efficiency and accuracy of the scheme in the presence of anisotropies and heterogeneities.