Droplet-based microfluidic platforms have the potential to provide superior control over mixing as compared to traditional batch reactions. Ionic liquids have advantageous properties for metal nanoparticle synthesis as a result of their low interfacial tension and complexing ability; however, droplet formation of ionic liquids within microfluidic channels in a two-phase system has not yet been attained because of their complex interfacial properties and high viscosities. Here, breakup of an imidazolium-based ionic liquid into droplets in a simple two-phase system has for the first time been achieved and characterized by using a microchannel modified with a thin film fluoropolymer. This microfluidic/ionic liquid droplet system was used to produce small, spherical gold (4.28 ± 0.84 nm) and silver (3.73 ± 0.77 nm) nanoparticles.