We examine the protein distribution within an electrospun polymer nanofiber using polyvinyl alcohol and bovine serum albumin as a model system. We hypothesize that the location of the protein within the nanofiber can be controlled by carefully selecting the pH and the applied polarity of the electric field as the pH affects the net charge on the proteins. Using fluorescently labeled BSA and surface analysis, we observe that the distribution of BSA is affected by the pH of the electrospinning solution. Therefore, we further probe the relevant forces on the protein in solution during electrospinning. The role of hydrodynamic friction was assessed using glutaraldehyde and HCl as a tool to modify the viscosity of the solution during electrospinning. By varying the pH and the polarity of the applied electric field, we evaluated the effects of electrostatic forces and dielectrophoresis on the protein during fiber formation. We surmise that electrostatic forces and hydrodynamic friction are insignificant relative to dielectrophoretic forces; therefore, it is possible to separate species in a blend using polarizability contrast. A coaxial distribution of protein in the core can be obtained by electrospinning at the isoelectric point of the protein, whereas surface enrichment can be obtained when the protein carries a net charge.