In this study, we present a novel approach for enhancing the performance of Quercetin-loaded nanofiber drug delivery systems through the modification of Polycaprolactone (PCL) solution using Cold Atmospheric Plasma (CAP) prior to electrospinning. CAP treatment was applied to PCL solutions for varying durations, namely, 0.5, 1, and 3 min. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) collectively demonstrate that CAP application and QU loading induce morphological changes in nanofibers, facilitating the creation of drug delivery systems with modified fiber diameters, devoid of bead formation. CAP treatment duration correlates with varying fiber diameters, with the longest treatment (3 min) producing the largest fibers (1324 ± 387 nm). Concurrently, the incorporation of quercetin (QU) into the PCL nanofibers resulted in reduced fiber diameter. These observations emphasize the pivotal role of CAP modification in tailoring nanofiber size and morphology. Notably, minimal peak shifts indicate no significant molecular structure changes in PCL nanofibers compared to PCL solutions, assuring the absence of unwanted chemical modifications or degradation during electrospinning. Furthermore, specific QU peaks are undetectable in Fourier-transform infrared (FTIR) spectra, suggesting dispersed or amorphous QU molecules within the nanofibers. Additionally, X-ray diffraction (XRD) results demonstrate that CAP treatment does not alter the crystalline structure of the PCL nanofiber drug delivery system. Crystalline planes of PCL remain unchanged, affirming stability under CAP treatment conditions. Water contact angles indicate that CAP treatment affects nanofiber hydrophobicity, with shorter CAP treatment times rendering more hydrophilic surfaces. Cumulative QU release percentages vary, with PCL/CAP-0.5-QU exhibiting the highest release at 56 ± 2.2 %, surpassing unmodified PCL/QU. Moreover, cell viability remains comparable or slightly increased when QU is incorporated into CAP-treated PCL nanofibers, suggesting potential mitigation of cytotoxic effects induced by CAP treatment. The combination of QU and CAP treatment enhances cancer cell viability reduction, QU release from nanofibers, and drug loading efficiency in a synergistic manner.