Quantification of mass transfer processes across micro-porous membranes can give valuable insight in applications of industrial and medical relevance. In this paper, a hybrid lattice Boltzmann-Finite differences (LBM-FD) code with non-uniform grid that simulates the mass transfer on a chip-like micro-device with an embedded micro-porous membrane has been developed. The model is validated showing good agreement with results of the Graetz-Leveque problem, even for Péclet numbers above 106, where conventional numerical methods fail to predict the correct behavior. The errors obtained in our simulations are below 1%. Simulations of the micro-porous membrane model in two and three dimensions show a linear scaling of the average Sherwood number with the number of pores and a value 1/3 of the scaling exponent of the Péclet number.