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Emulsion electrospinning is a method of modifying a fibers’ surface and functional properties by encapsulation of the bioactive molecules. In our studies, bovine serum albumin (BSA) played the role of the modifier, and to protect the protein during the electrospinning process, the W/O (water-in-oil) emulsions were prepared, consisting of polymer and micelles formed from BSA and anionic (sodium dodecyl sulfate–S) or nonionic (Tween 80–T) surfactant. It was found that the micelle size distribution was strongly dependent on the nature and the amount of the surfactant, indicating that a higher concentration of the surfactant results in a higher tendency to form smaller micelles (4–9 µm for S and 8–13 µm for T). The appearance of anionic surfactant micelles reduced the diameter of the fiber (100–700 nm) and the wettability of the nonwoven surface (up to 77°) compared to un-modified PCL polymer fibers (100–900 nm and 130°). The use of a non-ionic surfactant resulted in better loading efficiency of micelles with albumin (about 90%), lower wettability of the nonwoven fabric (about 25°) and the formation of larger fibers (100–1100 nm). X-ray photoelectron spectroscopy (XPS) was used to detect the presence of the protein, and UV-Vis spectrophotometry was used to determine the loading efficiency and the nature of the release. The results showed that the location of the micelles influenced the release profiles of the protein, and the materials modified with micelles with the nonionic surfactant showed no burst release. The release kinetics was characteristic of the zero-order release model compared to anionic surfactants. The selected surfactant concentrations did not adversely affect the biological properties of fibrous substrates, such as high viability and low cytotoxicity of RAW macrophages 264.7.