Development of hybrid formulations of hydrogels, antioxidants, and nanoemulsions containing polyunsaturated fatty acids is highly demanding. Herein, we report the formulation of quercetin-loaded oil-in-water nanoemulsions fabricated with surfactants like Tween 20 (nonionic), sodium salt of lauroyl sarcosine (anionic), and 3-(N,N-dimethylmyristylammonio)propanesulfonate (zwitterionic) for controlling autoxidative degradation of linoleic acid. Having a droplet size <200 nm, nanoemulsions containing anionic and zwitterionic surfactants were more effective in controlling lipid peroxidation at 37 °C. The size of their hybrid alginate capsules ranged from 2.00 to 2.30 mm that released quercetin and scavenged DPPH· (1,1-diphenyl-2-picrylhydrazyl) in saline media with a free radical scavenging activity of ∼80% from capsules rich in zwitterionic surfactants. High percent swelling of capsules (approximately 600–700%) and >90% percent recovery make the capsules highly robust. These formulations have potential to provide promising platforms for the enhancement of shelf life of linoleic acid and rational formulation of quercetin-containing supplements in food and pharmaceutical industries.