Extra-virgin olive oil (EVOO) is a chemically complex lipid matrix whose minor constituents—especially phenolic secoiridoids—drive sensory quality, oxidative stability, and health benefits. However, these bioactives are vulnerable to heat, light, oxygen, and pro-oxidant metals during processing and distribution, while the high cost of EVOO often makes it a target for adulteration and mislabeling. This review critically assesses nano-enabled, food-grade strategies that (i) preserve phenolics and aroma compounds through nanoencapsulation, inclusion complexes, Pickering stabilization, and structured lipid systems; (ii) control their release and bioaccessibility during digestion; and (iii) enhance authenticity verification via sensor-ready packaging, spectroscopy/chemometrics, and digital traceability systems (IoT, machine learning, blockchain). We align these innovations with the “product identity constraints” of the EVOO category and with official quality standards used in routine control (IOC/EU). Finally, we explore circular valorization of olive-mill by-products within food-centered biorefineries, outlining pathways to convert biomass into ingredients, materials, and energy, thus reducing environmental impacts. Research priorities are proposed to develop scalable, regulation-compliant nanotechnologies that extend shelf life and increase consumer trust without compromising EVOO category standards.