The expanding global population presents challenges for food production systems that extend beyond socio-economic considerations to encompass urgent climate-related disruptions. The agri-food sector is one of the largest contributors to greenhouse gas (GHG) emissions, emphasizing the critical need for sustainable practices aligned with Sustainable Development Goals. Crop processing by-products (CPBPs) from the food supply chain offer a promising approach for reducing environmental impact while generating social and economic benefits. This review examines the rational utilization pathways for sugarcane and citrus processing by-products, two of the most produced and underutilized crops globally, to mitigate GHG emissions. A comprehensive comparison of traditional and emerging management practices reveals that innovative CPBP utilization chains targeting food, chemicals, and energy provide substantial environmental advantages. Specifically, bioconversion processes, such as fermentation and anaerobic digestion for biogas and bioethanol production, exhibit notably lower emissions than chemical conversion methods. Moreover, the emerging development of integrated biorefinery systems demonstrates significant potential for low-emission utilization of CPBPs. These findings highlight the need for continued research into circular bioeconomy frameworks and standardized environmental assessment protocols to optimize CPBP valorization and contribute to global sustainability goals.