Reducing biogeochemical flows (e.g., reactive nitrogen [Nr]) is essential for a sustainable food system. Previous studies lack tailored strategies for Nr reduction in smaller-scale agricultural production. We developed a framework coupling material flow analysis and system dynamics modeling to establish a pathway for Nr reduction. We applied this framework to Fujian, southeast China, a mountainous and coastal province with fragmented small-scale agricultural and large-scale aquaculture production. Crops, livestock, and aquaculture accounted for 44.03%, 31.11%, and 23.69%, respectively, of Nr input in 2019. Thus, crop and livestock production accounted for approximately 70% of total Nr emissions. Only 8.66% of the total Nr inputs were recycled from livestock to cropland, and the Nr use efficiency of all three food categories was less than 20%. A balanced diet among residents increased (by 15.5%) Nr emissions, whereas minimized food loss and waste partially neutralized (reduced by 17.9%) the increase in Nr emission from dietary changes. By contrast, recycling kitchen waste, manure, and straw would eliminate 39.5% of the regional-food-system Nr emissions. We conclude that a circular agricultural system with Nr recycling is effective to reduce Nr input and emissions through more unified crop and livestock production in montane and coastal regions of Fujian.