The encapsulation of biomolecules and microorganisms into liposomes is useful for a number of biological and biomedical applications. For instance, it is possible to encapsulate pharmacological compounds to increase properties such as therapeutic effectiveness, circulation times, and biocompatibility. Here, we are interested in encapsulating yeast cells expressing translocating peptide molecules on their surfaces. This is with the final intention of separating out yeasts with translocating activity from those with other types of membrane activities. To accomplish this, we designed a microfluidic system for the synthesis of giant liposomes (100-150 µm in diameter) based on the droplet generation of double emulsions (water-in-oil-in-water) as templates. Giant liposomes were selected here due to their size, lipid structure (unilamellar), and the ability to control the internal content that closely mimic, albeit in a more simplified manner, the structural organization of living cells. The microfluidic device comprises a W/O/W-junction equipped with three sets of inlets, a main channel, and an output channel at an angle of 30°. The performance of the system was evaluated in silico by implementing a Two-Phase flow, Level set model where the flow rate ratios of the continuous and dispersed phases were altered until the droplet was formed. Next, interaction with yeasts was achieved by a Y-junction geometry with two 0.5 mm-length inlets at 45°. The interaction was simulated with the aid of a Mixture model. Maximum velocity was obtained at the center of the channel and a complete mixing at the outlet, which indicates high interaction levels. Finally, we implemented an inertial geometry for the separation of the liposomes with encapsulated yeasts, which is currently under simulation via Euler-Euler and Particle Tracing models.