Growing populations and the increasing use of existing resources has led to growth in organic waste emissions. Therefore, a sustainable approach to managing this waste has become a major concern in densely populated areas. Biological treatment is an efficient method for reducing the amount of organic waste, and for producing energy. A large number of biogas plants and compost facilities that use organic waste as a substrate for electricity and fuel production are being built around the world. The biological treatment process in these plants produces large amounts of organic waste, and there is therefore a growing need to find a sustainable use for this material. Organic waste, such as biogas residues and compost can be a valuable fertilizer for agricultural soils. They can serve as a source of plant nutrients and can also improve soil structure and water holding capacity. However, as organic residues are known to contain both heavy metals and organic contaminants there is a need for long term field experiments to ensure that soil and plant quality is maintained. In order to investigate the potential risks and benefits of using organic waste in agriculture, an 8 year field experiment was established in central Sweden. Under realistic conditions, compost and biogas residues from source-separated household waste were compared with traditional mineral fertilizer. We examined crop yield and soil chemical and microbiological properties. The main conclusion from the field experiment was that biogas residues resulted in crop yields almost as high as the mineral fertilizer NPS. In addition, several important soil microbiological properties, such as substrate induced respiration, potential ammonium oxidation and nitrogen mineralization were improved after application of both biogas residues and compost. Moreover, no negative effects could be detected from using either of the organic wastes. In particular the genetic structure of the soil bacterial community appeared to resist changes caused by addition of organic waste.