Organic farming is being proposed as an option to reduce nutrient losses and to make more careful soil and nutrient use than conventional agriculture. We studied the effect of organic versus conventional cropping on the dynamics and use efficiency of nitrogen (N), phosphorus (P) and potassium (K) using a long term field experiment where the following cropping systems are being compared since 1978: Two organic (bio-dynamic (DYN), bio-organic (ORG)), two conventional systems (CON with mixed organic and mineral fertilization, MIN with exclusively mineral fertilizers) and an unfertilized control (NON). Different forms and amounts of fertilizer applied in conjunction with different plant protection strategies affected the yields. As a result, systems differ in nutrient budgets calculated as difference between nutrient input through fertilizers and removal by harvested products. Over the complete experimental duration average annual N and K budgets were negative for all systems. Phosphorus budgets were negative for NON, DYN, ORG and MIN and positive for CON. This affected soil properties related to the dynamics of N, P and K. Total organic C and N contents follow the order NON