airy farming is a multi-billion {USD} industry that provides essential food products. At the same time, the millions of animals that this industry oversees generate a massive environmental footprint (affecting air, land, and water quality). Specifically, livestock manure is a carbon- and nutrient-rich waste stream that is routinely used as fertilizer. This practice enables nutrient recycling but also leads to emissions of greenhouse gases and to nutrient pollution of soils and waterbodies. Mitigating these environmental impacts requires investment in manure processing technologies; identifying and prioritizing investment strategies requires understanding inherent conflicts (trade-offs) and synergies that exist between economic and environmental impacts. In this work, we present a conflict analysis and resolution framework that integrates techno-economic analysis (TEA), life cycle assessment (LCA), and supply chain (SC) optimization. We use this framework to investigate deployment scenarios of manure processing pathways in the Upper Yahara watershed region of Wisconsin; here, we evaluate LCA metrics (GHG emissions, ammonia emissions, fossil energy use, and nutrient pollution) and TEA metrics (cost and revenue) for different pathways that include manure collection, storage, application, and processing steps. The LCA and TEA metrics are embedded within a SC optimization model that makes decisions on technology selection and geographical placement and on product transport in the study area. A conflict resolution procedure is used to explore trade-offs associated with these decisions and to identify optimal compromise solutions that best balance trade-offs. Our results reveal that there exist non-obvious conflicts and synergies between the explored metrics that can be exploited to mitigate multiple impacts simultaneously. We also find that the deployment of a diverse set of technologies is needed to fully resolve conflicts. The impact of emerging technologies (ultrafiltration and reverse osmosis) and government incentives is also discussed.