Unlike conventional cropping systems, which are characterised by targeted short-term fertility management, organic farming systems depend on long-term increase in soil fertility and promotion of soil biodiversity. This study sought to investigate long-term effects of organic matter inputs on various cropping systems in a 10-year-old experiment. Results show that in the long-term high C and N inputs enhance microbial activity. Microbial biomass N and the potential nitrification rate were higher in cropping systems based on green manure than in those reliant on inputs from animal manure and mineral fertilizer. Soil microbiological properties were affected by the individual crops in the rotation. The high microbial activity with increased organic matter inputs did not transform to enhanced crop productivity