In this study, biocompatible scaffolds containing plant-derived active compounds were designed for tissue engineering applications in medicine, aiming to improve cell proliferation and behavior under laboratory conditions. In this regard, genistein was extracted from soybean residue and nanoencapsulated using polycaprolactone (PCL) via the coacervation method. Finally, biocompatible nanofibers composed of gelatin (GE) and polyvinyl alcohol (PVA) were synthesized by electrospinning, incorporating genistein nanoparticles. Experiments were conducted using high-performance liquid chromatography (HPLC), UV-Vis spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy (FTIR), and mechanical testing. The biological effects and cell viability on genistein-loaded scaffolds were assessed using the MTT assay. The synthesized sample exhibited non-toxicity and significant adhesion to L929 cell line. In conclusion, the described biocompatible system could serve as an intelligent drug delivery tool for tissue engineering applications in laboratory settings.