There is disclosed a method for preparation of substrate for use in anaerobic digestion of organic waste. The method can be executed in a substrate pretreatment system, the method comprising: loading of a substrate into the substrate pretreatment system, mixing the substrate with liquid; heating the substrate and liquid to a pre-determined processing temperature; exposing the mixture to radiation; transferring the processed substrate to a bioreactor, during the heating, the method further comprises: degassing the mixture using vacuum extraction; and circulating the mixture past an ultrasonic hydrodynamic radiator.