An ideal agricultural system should both maximize food production and minimize undesirable effects on the environment. The long-term Apelsvoll cropping system experiment, located in southeast Norway, was used in this study, to compare yields, major N flows (in particular measured leaching/runoff losses) and the N loss-to-food production ratios (LFP-ratios) in six different cropping systems over a 4-year period. The experiment included three systems with cash-cropping (CA1: conventional arable farming; CA2: arable farming practice with environmentally sound management; OA: organic arable farming with 25% of the area as green manure, and three systems with both arable and fodder crops, representing mixed dairy production (CM: conventional farming practice with 50% grass–clover ley; OM1: organic farming with 50% grass–clover ley; OM2: organic farming with 75% grass–clover ley). The forage production was assumed to be used for milk and meat production, in amounts calculated on the basis of available feed and estimated requirements for dairy cattle. All farm produce (cereals, potatoes, milk and meat) was converted into metabolizable energy for human consumption. Organic cropping gave significantly lower yields than conventional cropping, for both arable and mixed dairy systems, most likely due to sub-optimal plant nutrition and the lack of plant protection in the organic systems. The average net energy production in CA1 and CA2 was 2.4–5.3 times greater than that in the other systems, which illustrates the energy costs of taking 25% of the area out of food production to produce green manure (OA) and the energy cost of including an extra trophic level in the nutrient chain (CM, OM1 and OM2). Only CA2 and CM appeared to have a balanced N budget, whereas the other systems all had N deficits, in particular CA1 and OA. The total N losses to drainage were largest from CA1, but not significantly larger than those from OA, which had the largest N runoff of the systems, most likely due to the green manure in its rotation. The conventional system with environmentally sound management (CA2) had the lowest LFP-ratios overall. Among the arable cropping systems, the organic system with 25% green manure (OA) had the highest LFP-ratios. The mixed dairy systems had generally higher LFP-ratios than the arable systems. Including leaching/runoff N losses in the LFP-ratio, CA1, CA2, OA, CM, OM1 and OM2 appeared to lose 0.6, 0.4, 1.1, 0.9, 1.2 and 1.1 kg N, respectively, per GJ of produced metabolizable energy for human consumption.