The present invention concerns an anaerobic digestion of animal manures, energy crops and similar organic substrates. The process is capable of refining nutrients comprised in the digested biomass to fertilizers of commercial quality. The invention also provides a method for oprocessing animal carcasses or fractions thereof including meat and bone meal etc., with the objective of providing an alternative means for processing the organic waste material of animal origin while at the same time facilitating the production of fertilizers. The risk of spreading BSE prions or any other prions to animals or humans is thus substantially reduced if not eliminated. The biogas and slurry separation system according to the present invention is preferably integrated with the operations of animal husbandries into a total concept in which the internal and external performances of animal husbandries are optimised. The internal performances concern quality aspects related to the management of the animal houses and include industrial hygiene, animal welfare, gaseous and dust emissions and food safety. The external performances concern mainly energy production and emissions to the environment of nutrients and greenhouse gases and the sale of high quality food product.