Agri-food waste, such as seeds, pulp, and fruit and vegetable peels, is rich in bioactive compounds; however, its stability and functionality are limited by traditional extraction methods and its sensitivity to external factors. This study systematically analyzed 68 experimental studies published in Scopus and ScienceDirect between 2020 and 2025, focusing on the valorization of agri-food waste through ecological techniques for the extraction and microencapsulation of bioactive compounds (phenolic compounds, flavonoids, anthocyanins, and other metabolites of functional interest) and their application in food. The literature reviewed indicates that extraction using ultrasound, microwaves, subcritical water, and supercritical fluids improves the yield and quality of bioactive compounds, reducing extraction time, energy consumption, and environmental impact. Furthermore, hybrid approaches (ultrasound + microwaves) can increase yield by up to 52% compared to individual techniques. Microencapsulation using protein and polysaccharide matrices allows for efficiencies greater than 90%, preserves the stability of the compounds for up to 90 days, and improves their bioaccessibility (25–95%). The incorporation of these bioactive compounds into food matrices not only increases the phenolic content and antioxidant capacity in foods such as yogurt, cookies, and meat products, but also reduces oxidation processes, extending their shelf life. In general, green extraction combined with microencapsulation constitutes a sustainable and efficient strategy that maximizes the recovery, stability, and functionality of bioactive compounds, promoting the circular economy and the development of functional foods. However, limitations remain that will need to be addressed in future research, including those identified by the bibliometric analysis and others observed directly in the studies reviewed. • Agri-food waste: severe environmental impacts, but rich in bioactive compounds. • Ultrasound and microwaves: higher yield, less time, and energy compared to conventional extraction. • Microencapsulation improves the stability, release, and bioaccessibility of bioactive compounds. • Bioactive compounds improve functionality in yogurt, cookies, and meat products.
Yata-Franco et al. (Sun,) studied this question.