The agri-food sector produces a huge amount of agri-food wastes and by-products, with a consequent great impact on environmental, economic, social, and health aspects. The reuse and recycling of by-products represents a very important issue: for this reason, the development of innovative recovery and extraction methodologies must be mandatory. In this context of a circular economy, the study of green extraction techniques also becomes a priority in substitution of traditional extraction approaches. This review is focused on the recovery of chlorogenic acids from agri-food wastes, as these compounds have an important impact on human health, exhibiting several different and important healthy properties. Novel extraction methodologies, namely microwave and ultrasound-assisted extractions, supercritical fluid extraction, and pressurized-liquid extraction, are discussed here, in comparison with conventional techniques. The great potentialities of these new innovative green and sustainable approaches are pointed out. Further investigations and optimization are mandatory before their application in industrial processes.