This study examined the capabilities of zein-based nanoparticles for the co-delivery of quercetin and α-tocopherol. The results demonstrated an optimal encapsulation efficiency of 96% with an average particle size of 50−320 nm, highlighting the proficiency of the method. Over 60 days, the retention release profiles showed gradual reductions, with the Zein/Que/Toc (20:1:1) and Zein/Que/Toc (20:1:25) formulations exhibiting distinct dynamics. In vitro analyses revealed controlled release, with quercetin reaching 79.7% and α-tocopherol reaching 60.4% after 8 h. The Zein/Que/Toc (20:1:5) combination exhibited a notable release of 73.1% over the same span, indicating a synergistic or stabilizing interplay between the co-encapsulated agents, which is beneficial for digestion. ATR-FTIR, rheology, and fluorescence spectroscopy investigations demonstrated key molecular interactions, including hydrogen bonding and hydrophobic forces. The integration of surfactants enhanced the photostability and retention of both bioactive compounds. This study emphasizes the vast potential of zein-based nanoparticles for bioactive co-delivery, with the Zein/ Que/Toc (20:1:5) formulation emerging as a viable candidate. These findings have implications for the pharmaceutical, nutraceutical supplement, drug, and functional food domains.