Mesoporous separator membranes based on poly(vinylidene fluoride-co-trifluoroethylene), PVDF-TrFE, were prepared through the removal of ZnO nanoparticles from the polymer matrix composite. Different filler concentrations were used, and the evaluation of the morphology, mechanical properties, uptake and ionic conductivity of the membranes were demonstrated that they depend on initial ZnO content in the composite. On the other hand, the vibration peaks characteristics of PVDF-TrFE and the thermal properties are independent on initial filler content. The membrane with the best ionic conductivity, 1.6 mS/cm, is the one prepared after 70 wt.% ZnO removal. The separator membranes were assembled in Li/C-LiFePO4 half-cells exhibiting good rate capability and cycling performance, the best battery performance being obtained for the PVDF-TrFE after 70 wt.% ZnO removal. The good performance of the developed separators was also demonstrated in full battery cells. Thus, a way to tailor membrane mesoporosity is presented and it is shown that the obtained membranes represent suitable separators for lithium-ion battery applications.