The biological activity of natural plant-oil-based nanostructured lipid carriers (NPO-NLCs) can be enhanced by the encapsulation of bioactive compounds, and they in turn can improve topical delivery of the drugs. Quercetin (QR), a vital plant flavonoid, expresses antibacterial properties, and we recently showed that empty NPO-NLCs also have antimicrobial activity. The main objective of this study was to evaluate the synergetic effect of loading natural plant-oil-based nanostructured lipid carriers with quercetin (QR-NPO-NLCs) as a topical delivery system for the treatment of bacterial skin infections. Five nanostructured lipid carrier systems containing different oils (sunflower, olive, corn, coconut, and castor) were engineered. The particles’ stability, structural properties, bioavailability, and antimicrobial activity were studied. NLCs with an average size of <200 nm and Z-potential of −40 mV were developed. Stable QR-NPO-NLCs were obtained with high encapsulation efficiency (>99%). The encapsulation of QR decreased cytotoxicity and increased the antioxidant effect of nanocarriers. An increase in antibacterial activity of the systems containing QR was demonstrated against Staphylococcus aureus. QR-NPO-NLCs could transport QR to an intranuclear location within HaCaT cells, indicating that QR-NPO-NLCs are promising candidates for controlled topical drug delivery.