The design of biocompatible cell culture substrates and electrospun nanofibers can improve cell proliferation and behavior in laboratory conditions for tissue engineering applications in medicine. In this research, genistin was obtained by extracting from soybean meal powder, and then by adding polycaprolactone (PCL), genistin nanocapsules were prepared. For the first time, we used a lipophilic nanophase (encapsulated genistin) coated in a hydrophilic nanophase (gelatin /polyvinyl alcohol) as a dual nanosystem by the electrospinning method. In the approach, the nanofibers mimic the natural extracellular matrix, interact favorably with cells being cultured from one side, and raise the local concentration of a bioactive compound at the cell surface. The encapsulated drug which was inserted in fibers with a loading percentage of 92.01% showed appropriate and significant controlled release using high-performance liquid chromatography (HPLC). To prove the experiments, analysis using an ultraviolet–visible spectrometer (UV–Vis), 1H NMR spectrometer, Fourier transforms infrared spectrometer (FTIR), mechanical test, scanning electron microscope (SEM) and microscope transmission electron microscopy (TEM) was performed. The sample synthesized with 40% drug using the MTT method exhibited remarkable biological effects, viability, and non-toxicity. Additionally, significant proliferation and adhesion on the mouse fibroblast cell line L929 were observed within a 72-h timeframe.