Zein and gelatin-pectin nanofibers including carotenoid microemulsion were fabricated by emulsion electrospinnig. The microemulsion and feed solution properties, fiber morphology, carotenoid compounds and encapsulation efficiency were determined. The particle size ranges of microemulsion were narrow (190–206 nm) with homogeneous distribution. A low PDI value (0.251±0.02) showed a uniform size distribution. The zein solution properties except viscosity decreased with addition of the microemulsion, while all solution properties decreased for the gelatin-pectin solution. Scanning electron micrograph images showed that the addition of the microemulsion along with solvents significantly affected the electrospinning process, fiber diameter and morphology. As the microemulsion concentration increased, fiber production became more difficult or fiber could not be obtained. Electrospinability was better for zein solutions than the blend of gelatin-pectin solution. The highest encapsulation efficiency (%79.74) was achieved with zein nanofibers including the mixture of acetic acid:ethanol:water (30:40:30) and 40% microemulsion. In addition, gelatin-pectin nanofibers with 30% microemulsion were relatively obtained more smooth and thinner diameter, while the nanofibers had lowest encapsulation efficiency. Accordingly, the zein nanofibers and pectin-based nanofibers may be used as carrier vehicles for microemulsion containing bioactive compounds. They may be as a promising material in fortified foods and pharmaceuticals.