A key challenge is to increase sustainability in agriculture without yield loss. Organic agriculture uses no chemical fertilizers and pesticides. Instead, yield depends on nutrients released from organic inputs, and thereby on soil communities that drive soil carbon and nutrient cycling. However, these soil communities may need time to establish, resulting in lower yields during the beginning of this conversion. How carbon and nutrient cycling change during the conversion from conventional to organic agriculture is not well understood, but it may help us to understand, and eventually reduce, the yield gap. Here, we studied how carbon and nitrogen cycling change when converting conventional agricultural systems into organic agricultural systems. We used a chronosequence approach, where we collected soil samples from 37 organic fields, on both sand and clay soils, that have been converted from conventional to organic agriculture between 1 to 40 years ago and from neighboring conventional fields. Under controlled conditions we measured potential rates of carbon and nitrogen mineralization. Potential carbon mineralization and substrate induced respiration were higher in organic soils, but there was no effect of time since conversion. This might be explained by variation in abiotic factors such as soil organic matter content. We use our data to unravel how fast ecosystem processes change after the conversion of conventional into organic farming systems. Our findings will yield important insights how the performance of soil communities is changed during transition and this will help us to understand changes in crop yield.