At nanoscale length scales, the properties of particles change rapidly with the slightest change in dimension. The use of a microfluidic platform enables precise control of sub-100 nm organic nanoparticles (NPs) based on polybenzimidazole. Using hydrodynamic flow focusing, we can control the size and shape of the NPs, which in turn controls a number of particle material properties. The anhydrous proton-conducting nature of the prepared NPs allowed us to make a high-performance ion exchange membrane for fuel cell applications, and microfluidic tuning of the NPs allowed us subsequently to tune the fuel cell performance.