Objective: Due to rapid economic return, mixed crop-swine farming systems in Korea have become more intensive. Intensive farming practices often cause nutrient surpluses and lead to environmental pollution. Nutrient budgets can be used to evaluate the environmental impact and as a regulatory policy instrument for nutrient management. This study was conducted to select a nutrient budgeting approach applicable to the mixed crop-swine farms in Korea and suggest an effective manure treatment method to reduce on-farm nutrient production. Methods: In this study, we compared current and ideal gross nutrient balance (GNB) approaches of Organisation for Economic Cooperation and Development and soil system budget (SSB) approach with reference to on-farm manure treatment processes. Data obtained from farm census and published literature were used to develop the farm nutrient budgets. Results: The average nitrogen (N) and phosphorus (P) surpluses were approximately 11 times and over 7 times respectively higher in the GNB approaches than the SSB. After solid-liquid separation of manure, during liquid composting a change in aeration method from intermittent to continuous reduced the N and P loading about 50% and 47%, respectively. Although changing in solid composting method from turning only to turning+aeration improved the N removal efficiency by 30.5%, not much improvement in P removal efficiency was observed. Conclusion: Although the GNB approaches depict the impact of nutrients produced in the mixed crop-swine farms on the overall agricultural environment, the SSB approach shows the partitioning among different nutrient loss pathways and storage of nutrients within the soil system; thus, can help design sustainable nutrient management plans for the mixed cropswine farms. The study also suggests that continuous aeration for liquid composting and turning+aeration for solid composting can reduce nutrient loading to the soil.