About half of all N and P loads to Swedish waters originate from agriculture and must decrease to reach environmental goals. Studying nutrient management at farm level can provide an understanding of nutrient recycling and the risk of losses. In a survey of organic and conventional dairy and arable farms in three southern counties of Sweden, farm-gate N and P balances and N use efficiency (NUE) were analysed. Crop distribution differed significantly between organic and conventional farms, with organic dairy farms having higher proportions of ley and pulse crops and organic arable farms having a much higher proportion of N-fixing crops than corresponding conventional farms. Conventional dairy and arable farms had on average 70% and 40% higher N surplus than corresponding organic farms. Farm-gate P surplus was larger on conventional dairy farms and much larger on organic arable farms, mainly due to purchase of P-rich organic fertilisers. Organic dairy farms had higher NUE than corresponding conventional farms, but the opposite was true for arable farms. However, in the southernmost county Skåne, where soil fertility and yield potential are high, NUE was similar on all arable farms. Total inputs of N and P were positively correlated with N and P surpluses, especially on dairy farms. Improved manure and crop residue management, reduced use of purchased mineral N fertilisers coupled to more uniform within-farm distribution of manure, use of catch crops, intercropping and organic fertilisers with appropriate N:P ratio are measures that can reduce farm nutrient surpluses and improve nutrient management on both organic and conventional farms.