The increasing need for healthier and functional foods has encouraged the advancement of innovative biotechnological techniques that adhere to reuse, recycle, and recovery concepts. These technologies are designed to improve the functionality and health advantages of food products while also encouraging sustainable practices in the agri-food industry. Ongoing recognition of the importance of environmental sustainability and the necessity to optimize the use of all resources has resulted in the development of different biotechnological approaches for handling agri-food by-products. These novel strategies seek to convert waste streams into useful bioproducts, promoting a more circular and efficient agri-food system. Bioprocess optimization, through integrating processes such as fermentation, extraction, and purification, enhances the efficiency of recovering and purifying the desired bioactive substances. By implementing integrated biorefineries and valorization clusters, the process of waste collection, processing, and market distribution can be seamlessly integrated, resulting in the formation of a circular economy model. These “Ways-to-Health” approaches aim to optimize the extraction and purification of physiologically active chemicals, hence facilitating the generation of novel, health-enhancing food and nutraceutical products. Incorporating these biotechnological factors into a circular bioeconomy framework facilitates the sustainable handling of agri-food by-products and waste. By utilizing the capabilities of these cutting-edge technologies, the industry may diminish its negative effects on the environment, generate additional sources of income, and aid in advancing a more robust and effective food system.