An 8-year-long field experiment (1998–2006) was established in Sweden with the aim of evaluating the effects of applying organic wastes in combination with mineral nitrogen (N) to agricultural soil. Sewage sludge (SS), biogas residues (BR) and municipal compost (CO) were applied annually at rates corresponding to 50 kg N/ha and supplementary mineral N fertilizer also applied at rates corresponding to 50 kg N/ha. The effects were evaluated by analysing crop yield and soil chemical and microbiological properties. The results showed that none of the fertilizers produced significantly higher yield of barley over the 8-year period compared to any other. Biogas residue proved to be particularly beneficial for the substrate-induced respiration (SIR) in soil and increased the proportion of active to dormant micro-organisms. Treatment with SS increased plant-available phosphorus (P-AL) and N mineralization (N-min), whereas CO increased the basal respiration (B-resp). Changes in the microbial community structure were assayed by terminal restriction fragment length polymorphism (T-RFLP); the T-RFLP signatures of the soil bacterial community were largely unaffected by the addition of organic waste. Of the chemical properties assayed, the largest increases were seen in P-AL, where SS produced the highest value. Treatments with the organic wastes showed no negative effects other than a slight decrease in B-resp induced by SS and BR. In conclusion, the microbiological activity in the soil responded more rapidly than the changes in the community structure and the chemical properties to changes in the soil environment.