The gas/liquid phase separation of CO2 from a water-methanol solution at the anode side of a µDirect-Methanol-Fuel-Cell (µDMFC) plays a key role in the overall performance of fuel cells. This point is of particular importance if the µDMFC is based on a “Lab-on-a-Chip” design with transient working behaviour, as well as with a recycling and a recovery system for unused fuel. By integrating a membrane-based micro contactor downstream into the µDMFC, the efficient removal of CO2 from a water-methanol solution is possible. In this work, a systematic study of the separation process regarding gas permeability with and without two-phase flow is presented. By considering the µDMFC working behaviour, an improvement of the overall separation performance is pursued. In general, the gas/liquid phase separation is achieved by (1) using a combination of the pressure gradient as a driving force, and (2) capillary forces in the pores of the membrane acting as a transport barrier depending on the nature of it (hydrophilic/hydrophobic). Additionally, the separation efficiency, pressure gradient, orientation, liquid loss, and active membrane area for different feed inlet temperatures and methanol concentrations are investigated to obtain an insight into the separation process at transient working conditions of the µDMFC.