The growing demand for sustainable food preservation drives interest in edible nanoemulsions encapsulating bioactive compounds. This study developed casein–lecithin-based nanoemulsions combining carvacrol (CV)—a compound with potent antimicrobial and moderate antioxidant activity—with vitamin E (VitE)—a powerful antioxidant—as multifunctional food coatings. Three formulations were prepared via homogenization: NE-CV (2% CV), NE-VitE (2% VitE), and NE-CV/VitE (1% each). Physicochemical characterization revealed monomodal size distributions (22.7–57.7 nm), with successful encapsulation confirmed by FTIR. NE-CV/VitE exhibited intermediate particle size (34.4 nm) and zeta potential (−19.8 mV). Antioxidant activity followed NE-VitE > NE-CV/VitE > NE-CV, with the co-encapsulated system preserving VitE’s radical scavenging (EC₅₀ 10.76 µL/mL, DPPH). Remarkably, NE-CV/VitE demonstrated enhanced antibacterial activity against E. coli, requiring half the CV concentration (0.07 mg/mL) versus NE-CV alone (0.15 mg/mL), while maintaining CV dose-dependent activity against S. aureus (0.30 mg/mL). Nanoencapsulation significantly reduced CV cytotoxicity in human lymphocytes at concentrations up to 50 μg/mL (48.8% cytostasis vs. 58.9% for free CV), with no genotoxic effects observed within this range, while preserving full bioactivity. In fresh minced pork over 6-day refrigerated storage, NE-CV/VitE coating maintained pH stability (5.65–5.75), preserved red color (a* values 6.24 vs. 4.99 uncoated), reduced lipid oxidation (TBARS 0.74 vs. 0.82 mg MDA/kg), and achieved a 99% reduction (2-log) in total viable counts versus uncoated controls. The CV/VitE co-encapsulated nanoemulsion represents an integrated, safe, and effective multifunctional preservation technology with synergistic antimicrobial enhancement and uncompromised antioxidant protection, offering a natural alternative for comprehensive food quality preservation.