The purpose of the paper is to determine the environmentally safe and economically feasible technology of biofertilizer production from the digestate including dewatering process. Methodological basis is based on the systematic approach to the determination of factors effected on the distribution of nutrients and pollutants between liquid and solid fractions after digestate separation. The paper analyzes modern technologies aimed at dewatering the digestate and reduction of its volume, showed their effectiveness. These technologies allow expanding the opportunities for commercialization of the digestate, increasing the cost of its transportation and application to the soil instead of complex fertilizers, using some valuable products. The results of the study showed that the ecological quality of the digestate is the highest as well as co-digested thermally pre-treated feedstock is used for solid-liquid separation in centrifuge with polymer addition as post-treatment approach to the flocculation. In order to increase efficiency of biofertilizer application the technological scheme of production process of granular fertilizers from digestate was proposed. Special feature of this scheme is in the use of phosphogypsum binder for the production of organo-mineral fertilizer that contributes phosphogypsum recycling in the waste management system.