Anaerobic digestion of farmyard manures may help farmers to produce bioenergy instead of using fossil fuels, support cycling of nutrients and reduce greenhouse gas emission. However, compared to pristine slurry, digested slurry has a reduced content of organic carbon which may impact the soil biota negatively due to substrate shortage. Our knowledge on these processes and their influence on soil quality is scarce. Hence, a field experiment with two organic cropping systems (grass-clover ley and arable system; at two slurry-application levels) was established in 2011, to study how application of digestates affects crop yields, soil characteristics and soil biota (earthworms, springtails, microbiota). The grass-clover system showed comparable yield levels over 3 years when digested slurry was compared to untreated slurry. Digested slurries had no influence on soil nutrient concentrations or on soil organic matter levels over the first 2 years. Application of high levels of manure increased the mortality of both surface-dwelling and soil-living earthworms just after application, but the long-term effect of manure application seemed more positive, especially at low application levels. Springtails and microorganisms seemed only little affected by application of digested slurry.