We discuss the integration of membrane emulsification and pervaporation processes for the continuous production of functional materials, such as silica-encapsulated magnetite nanoparticle clusters and asymmetric Janus nanoparticles, by the emulsion droplet solvent evaporation method, which has traditionally been performed in small-scale batch systems. An organic solvent containing primary magnetite nanoparticles (similar to 10 nm) coated with oleic acid was dispersed in a continuous aqueous phase by membrane emulsification, which enabled the consistent production of nanoparticle-laden solvent droplets of well-controlled size with narrow size distributions. The solvent was removed from the emulsion by pervaporation. Prior to complete solvent removal, the nanoparticle packing density within the clusters was a function of the residence time in the pervaporation unit. The final clusters formed, similar to 100-300 nm in size, exhibited the same superparamagnetic behavior as the primary nanoparticles, and were stable in aqueous media with a zeta potential of -70 mV at neutral pH. A facile method was used to coat the nanoclusters with a silica shell, providing sites for surface functionalization with a range of organic ligands. The nanoparticles and clusters were analyzed by a variety of techniques, including TGA, DLS, TEM, EDS, and SQUID. The effects of various parameters, such as the membrane dimensions and flow rate through the unit, on the mass transport rates were elucidated through a parametric modeling study. The applicability of the methods to the production of polymeric beads and more complex particles was demonstrated; to create Janus structures, organic polymer solutions were dispersed as droplets in continuous aqueous phases, and the solvent was subsequently evaporated. The Janus particles consisted either of polymeric cores with magnetite nanoparticles clustered as islands on their surfaces, or of two phase-separated polymers, each constituting half of any given polymeric particle.