In accordance with the PRISMA 2020 guidelines, a systematic review was conducted on the green extraction of bioactive compounds from fruit matrices through the integration of emerging technologies and natural deep eutectic solvents (NADES). Studies published between 2015 and 2025 were analyzed from databases such as Scopus and Web of Science, and 63 relevant studies were selected following a rigorous methodological evaluation process. The results demonstrate a growing scientific interest in the use of NADES due to their sustainable nature, low toxicity, and high extraction efficiency, particularly when combined with technologies such as ultrasound and microwaves. These synergies enhance yield, reduce energy consumption, and preserve the stability of polyphenols, flavonoids, and anthocyanins. Furthermore, the physicochemical properties of NADES, such as polarity and viscosity, together with operational factors, such as temperature and water content, significantly influence process efficiency, indicating that the combination of NADES with emerging technologies represents a promising alternative for agri-food valorization with potential application as functional ingredients and in clean-label systems. Moreover, it is established as a robust strategy for the development of sustainable extraction processes with industrial scale-up prospects.