The bulk production of polymeric nanofibers is important for fabricating high-performance, nanoscale materials. Rotary jet spinning (RJS) enables the mass production of nanostructured fibers by centrifugal forces but may result in inconsistent surface morphologies. Because nanofiber performance is dependent upon its surface features, we asked which parameters must be optimized during production to control fiber morphology. We developed and tested a mathematical model that describes how the competition between fluid instability and solvent removal in RJS regulates the degree of beading in fibers. Our data suggest that solvent evaporation during the spinning process causes an increase in jet viscosity and that these changes inhibit both bead formation and jet thinning. The RJS was used to vary experimental parameters, showing that fiber beading can be reduced by increasing solvent volatility, solution viscosity, and spinning velocity. Collectively, our results demonstrate that nanofiber morphology and diameter can be precisely controlled during RJS manufacturing.