Abstract This paper studies the effect of mechanical pretreatment of NPKCa-containing waste (vegetable waste VW and thickened sewage activated sludge TSAS) on biogas production and agronomic quality of the digestates. The efficiency of this process was evaluated by the yield of methane during anaerobic co-digestion with bioadditive (cheese whey), as well as the nutrients content in digestates by using an agrochemical test. It was found that with increasing comminution intensity the particle size of the substrate decreases from 50 to 16 μm which causes an increase in biogas yield by ~30%. As a result, the carbon content in the digestates decreases from 72 to 44%, whereas nutrients content increases by, %TS: N – 3.4; P – 3.7; K – 3.7; Ca – 7.6. The grinded substrate was used for anaerobic digestion with the addition of various amounts of cheese whey. Obtained digestates have a stimulating effect on the growth of barley and peas plants. In particular, digestion with 3 wt% of whey had the maximum impact on plant yield (+0.3–0.4 t ha−1 compared to control). Moreover, the combination of vigorous comminution with the addition of whey leads to a significant reduction in the fermentation duration (up to 4 times) and increases biogas production by 41%. Obtained digestates can be considered as organo-mineral fertilizers since they contain up to 43% of the total amount of NPKCa and meet the requirements for the content of heavy metals under Ukrainian legislation.