The aim of the project is to develop and implement a complete technological line for pretreatment of substrates from agro-food industry by using hydrodynamic and lowtemperature disintegration in an innovative hybrid configuration. Until now, the processes were used separately for waste activated sludge generated in wastewater treatment plants. The proposed technology is dedicated for implementation in both agricultural biogas plants and wastewater treatment plant (municipal biogas plants). The increased bioavailability of substrates for the methanogenic co-fermentation contributes to increasing biogas production, improving rheological quality and dewatering efficiency of digested sludge, as well as decreasing the amount of digested sludge for further management. Simultaneously, energy balance and profitability of biogas plants will be improved. Besides, the process of substrates disintegration influences quality of the sludge liquor from a dewatering unit and subsequently an approach for the liquor treatment. The issue of the sludge liquor treatment and recovery of nitrogen and phosphorous as struvite complements the necessary knowledge for a user of the proposed technology. The research work on disintegration, digestion and reject water treatment will be carried out in a laboratory scale, and then revised in full scale on the prototype assembly. The mobile disintegration unit could be implemented as a testing product in large objects or a final product in small-scale objects. At each stage the proposed technology will be analyzed and optimized using a computer model, and technological, energy and cost criteria will be used to select the best solutions. The simulation model extended with environmental assessment will create an advanced estimation tool being a novelty in both agricultural and municipal biogas plants.