In this study, nanofibers against pro dimorphic fungal sessile growth were developed. Quercetin was successfully encapsulated within poly(d,l-lactide-co-glycolide)-poly(epsilon-caprolactone) nanofibers using an electrospinning technique. Field emission scanning electron microscopy, fluorescent microscopy, and Fourier-transformed infrared spectrometer were used to confirm the formation as well as encapsulation of quercetin within the nanofibers. These fabricated nanofibers were further evaluated to determine the effectiveness of the antibiofilm activity against Candida albicans. The cytocompatibility of quercetin-encapsulated nanofibers was found to be similar to control and pure polymeric nanofibers based on 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay against human embryonic kidney (HEK-293) cell lines. These fabricated nanofibers potentially could be used as coatings on biomedical devices to inhibit microbial contaminations.