Electrospun multilayer nanofiber matrices developed using β-cyclodextrin, poly(vinyl alcohol), and poly(lactic-coglycolic) acid effectively encapsulated the hexanal biomolecule and facilitated its controlled release. The multilayer nanofiber matrices loaded with hexanal (overlay method) are characterized through scanning electron microscopy (171 nm), transmission electron microscopy (73 nm), Fourier transform infrared spectroscopy (peak at 1716 cm −1 corresponds to hexanal), X-ray diffraction (12.13 and 18.69°), and thermogravimetric analysis (340 °C). Fruits treated with hexanal-loaded multilayer nanofiber matrices by the overlay method recorded a lower loss in physiological weight, pH, total soluble solids, and total sugar content (17.61%, 5.15, 20.05°Brix, 17.32%, whereas in control 26.99%, 5.75, 23.08°Brix, and 21.34%, respectively, on 21st day of observation), and furthermore, the firmness, titratable acidity, and vitamin C (11.86 N/m, 0.54, and 8.53%) were higher than those of control (6.12 N/ m, 0.38, and 5.09%, respectively). The shelf life of mango fruits (var. Alphonso) treated with multilayer nanofiber matrices was extended up to 23 days compared to that of the control fruits (12 days). Thus, the overall results suggested that multilayer nanofiber matrices effectively encapsulate hexanal and regulate its release slowly, which could be effectively used to enhance the physical and biochemical components and shelf life of fruits.