Worldwide, a massive amount of agriculture and food waste is a major threat to the environment, the economy and public health. However, these wastes are important sources of phytochemicals (bioactive), such as polyphenols, carotenoids, carnitine, coenzymes, essential oils and tocopherols, which have antioxidant, antimicrobial and anticarcinogenic properties. Hence, it represents a promising opportunity for the food, agriculture, cosmetics, textiles, energy and pharmaceutical industries to develop cost effective strategies. The value of agri-food wastes has been extracted from various valuable bioactive compounds such as polyphenols, dietary fibre, proteins, lipids, vitamins, carotenoids, organic acids, essential oils and minerals, some of which are found in greater quantities in the discarded parts than in the parts accepted by the market used for different industrial sectors. The value of agri-food wastes and by-products could assure food security, maintain sustainability, efficiently reduce environmental pollution and provide an opportunity to earn additional income for industries. Furthermore, sustainable extraction methodologies like ultrasound-assisted extraction, pressurized liquid extraction, supercritical fluid extraction, microwave-assisted extraction, pulse electric field-assisted extraction, ultrasound microwave-assisted extraction and high hydrostatic pressure extraction are extensively used for the isolation, purification and recovery of various bioactive compounds from agri-food waste, according to a circular economy and sustainable approach. This review also includes some of the critical and sustainable challenges in the valorisation of agri-food wastes and explores innovative eco-friendly methods for extracting bioactive compounds from agri-food wastes, particularly for food applications. The highlights of this review are providing information on the valorisation techniques used for the extraction and recovery of different bioactive compounds from agricultural food wastes, innovative and promising approaches. Additionally, the potential use of these products presents an affordable alternative towards a circular economy and, consequently, sustainability. In this context, the encapsulation process considers the integral and sustainable use of agricultural food waste for bioactive compounds that enhance the properties and quality of functional food.