Aims - Intercropping increases aboveground and belowground crop productivity, suggesting potential for carbon sequestration. Here we determined whether intercropping affects decomposition of soil organic matter (SOM) and root litter. Methods - We measured in the laboratory and the field the breakdown of SOM, root litter of maize, wheat, or faba bean, litter mixtures, and a standard substrate (compost) in soils from a long term intercropping experiment. Results - Soil organic matter from intercrop plots decomposed faster than SOM from monocrop plots, but compost decomposed at similar rates in different soils. Faster SOM decomposition was associated with lower soil C:N ratio. Root litter mixtures of maize and wheat decomposed as expected from single litters, but litter mixture of maize and faba bean decomposed faster than expected, both in the laboratory and in the field. Root litter decomposed slowly in maize/wheat intercrop soil compared to the two monocropped soils in the laboratory, but the effect was absent in the field. Conclusions - Intercropping increases SOM decomposition, presumably through reduced SOM recalcitrance resulting from lower C:N ratio, higher litter input and better N retention. Depending on the crop combination, also non-additive effects of root litter mixing can enhance organic matter decomposition in intercropping soils.