To probe the complexity of biological systems, large numbers of independent experiments are needed to gather statistically reliable information. A platform that performs these experiments at high-throughput demands precise control over the formation and delivery of microcapsules. Microfluidics enables passive and active modes of droplet formation, manipulation, and mixing. Aqueous- and organic-based emulsions serve as well-defined compartments that encapsulate target materials (e.g., cells, reagents, nucleic acid, and nanoparticles) in femto- to picoliter volumes surrounded by an immiscible fluid. In this work, we demonstrate a high-throughput PDMS-based microfluidic device for fabrication and control of uniform micron-size water-in-oil and oil-in-water emulsions. Passive and active modes of droplet generation (i.e., hydrodynamic flow focusing and electrospray, respectively) are utilized to form droplets in the size range of 1 to 100 μm. We also leverage dielectrophoretic forces to steer the microemulsions across flows of organic or inorganic phases. The dielectrophoretic force provides high-speed separation with no moving elements and does not require droplet charging. Two electrode designs of AC- and DC-based circuits incorporated into the PDMS block are proposed. We investigate the effect of frequency and voltage on the degree of deflection and separation efficiency of the emulsions. We show that the fabricated microcapsules can be used as templates to build synthetic lipid bilayer model membranes that more accurately mimic physiological conditions. In addition, our microfluidic-based device integrated with on-board electronics can be used as an essential component in high-speed screening bioassays.