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Regions of intensive farming are often associated with large nutrient surpluses emitted from agri-food systems (AFS). Agricultural transitions require reaching a balance between the roles of livestock systems in producing high-quality protein and organic fertilizers, while mitigating pollutant emissions. However, effects of the relative percentages of ruminants and monogastric animals in regions with high livestock density on their food production and environmental impacts remain unexplored. While most research on nutrient flows in AFS focuses mainly on large scales (e.g. continents, countries), the territorial scale remains underexplored. This study aimed to develop an integrated, down-scaled (NUTS 3) assessment framework to analyze nitrogen (N) and energy flows in two territories with differing compositions of ruminants and monogastric animals. Using material flow analysis based on public data, we examined two neighboring territories in Brittany, France. We assessed their environmental impacts, N flows, and energy functioning. The two territories imported 38% and 62% of N in feed, respectively, producing enough animal products to meet 9–13 times their local need for animal-based food. The results suggest that the area of external agricultural land required for producing feed imports is as large as the used agricultural area in the territory. Energy from biogas production represented 20% of the total energy input of the AFS. The territory with a more balanced share of ruminants and monogastric animals had higher livestock N conversion efficiency (37% vs. 30%) but lower total N self-sufficiency (21% vs. 12%) than the more ruminant-dominant territory. These results provide novel insights into environmental impacts of multiple combinations of ruminant and monogastric animal systems in similar territories. Such results could be useful for local policymakers and AFS stakeholders to help them understand the impacts of different livestock combinations on N and energy flows in their territory. The study also provides a framework for subnational-scale assessments, which are not well represented in public data. This framework is a key first step to facilitate the transition toward more sustainable AFS. • Nitrogen and energy flows in two livestock agri-food systems were compared. • Detailed multi-scale analysis of 69 nitrogen flows was performed. • N-use efficiency averaged 46% for the two agri-food systems. • Energy from biogas production was 20% of total energy input.