In electro-membrane processes, a pressure difference may arise between solutions flowing in alternate channels. This transmembrane pressure (TMP) causes a deformation of the membranes and of the fluid compartments. This, in turn, affects pressure losses and mass transfer rates with respect to undeformed conditions and may result in uneven flow rate and mass flux distributions. These phenomena were analyzed here for round pillar-type profiled membranes by integrated mechanical and fluid dynamics simulations. The analysis involved three steps: (1) A conservatively large value of TMP was imposed, and mechanical simulations were performed to identify the geometry with the minimum pillar density still able to withstand this TMP without collapsing (i.e., without exhibiting contacts between opposite membranes); (2) the geometry thus identified was subject to expansion and compression conditions in a TMP interval including the values expected in practical applications, and for each TMP, the corresponding deformed configuration was predicted; and (3) for each computed deformed configuration, flow and mass transfer were predicted by computational fluid dynamics. Membrane deformation was found to have important effects; friction and mass transfer coefficients generally increased in compressed channels and decreased in expanded channels, while a more complex behavior was obtained for mass transfer coefficients.