This comprehensive investigation delves into the interconnectedness of different features of cardiometabolic syndrome, such as metabolic dysfunction‐associated steatotic liver disease (MASLD), atherosclerotic cardiovascular disease (ASCVD), and gut dysbiosis, highlighting the crucial role of nutraceuticals in their management and prevention. Given the significant overlap in the pathophysiology of these conditions, the treatment with nutraceuticals, especially those derived from agro‐food waste, offers a promising, sustainable, and innovative approach to healthcare. The 2030 Agenda for Sustainable Development and the One Health concept are key frameworks for selecting the most interesting supply chain for the production of nutraceuticals from agro‐food waste, ensuring environmental sustainability, and innovative agricultural practices. In this review, the therapeutic potential of kiwifruit and apples has been explored, detailing how their bioactive compounds, like polyphenols, fiber, pectin, kaempferol, phloretin, and phlorizin, may contribute to the management of MASLD, ASCVD, and gut dysbiosis. Various extraction methods for active ingredients, including chemical, water, and enzyme extractions, are analyzed for their respective benefits and drawbacks. By integrating scientific research, sustainable agricultural practices, and innovative extraction methods, we can develop effective strategies to combat these pervasive health issues. This holistic approach not only enhances individual health outcomes but also supports broader environmental and societal goals, promoting a healthier future for all.