A large percentage of world’s eutrophication is attributed to the livestock industry, which is responsible for producing over 14% of the global anthropogenic greenhouse gasses emissions (GHG). In Mexico, very few livestock producers have the necessary infrastructure to treat their livestock waste (LW) and most fail to comply with environmental regulations. The treatment of LW through a circular bioeconomy approach can mitigate these negative environmental impacts, while simultaneously producing value-added products. The present work aimed to characterize the spatial variation of the LW generated in cattle, swine, and poultry farms in Jalisco, México. Total nitrogen (TN), phosphorus (TP), and organic matter released from these production units were estimated, along with the associated GHG, considering the standard practice of uncontrolled release. An alternative management scenario using anaerobic digestion (AD) combined with microalgae-based wastewater treatment (MbWT) was evaluated by developing a software-based techno-economic analysis, showing that a centralized LW treatment system could represent a feasible solution to comply the legislation while generating high-protein biomass for animal feed. Besides, the reduction in GHG represents an opportunity for carbon credits trading in voluntary markets for livestock producers in México. Insights are provided regarding the economical, technical, and sociocultural challenges that must be overcome to transition towards more sustainable livestock production practices in Jalisco, México, and other developing regions around the globe.