High-throughput emulsion electrospinning is a technology that can enable practical nanofiber application for drug delivery. Core-shell structure of the electrospun fibers allows the encapsulation of the active pharmaceutical ingredients (APIs), protects their activity, and controls their release rate. However, electrospinning using high flow rates usually requires high electric fields that may negatively affect the activity of the biomolecules. Moreover charged APIs tend to migrate to the surface of the fibers during the electrospinning process leading to the high burst release. That is disadvantageous when long-term sustained release is needed. We have investigated the influence of the electrospinning parameters such as distances between the electrode and collector and the applied voltages to both, activity of the encapsulated proteins and their burst release. We have also tested the influence of number of the stabilizers, e.g. trehalose, pluronic, polyvinylpyrrolidone, on their ability to preserve the protein activity, and the influence of the different molecular weights of polyvinyl alcohol on the ability to sustain the release. Our results demonstrate the importance of the water phase composition to both activity and release and are critical for further understanding of the processes taking place during the emulsion electrospinning.