Under conditions of field production experiments, it was shown that the large-tonnage waste of hydrolysis production is the hydrolysis lignin (HL), which can act not only as a source of organic matter in organic or organic-mineral fertilizers, but also serve as a matrix for microorganisms, contributing to improvement of phytosanitary state of soils. It was shown that HL not only contributes to improvement of physicochemical properties of soils and replenishment of humus reserves, but also increases the resistance of plants to diseases, providing a yield increase by 10-20%. In this regard, the integrated use of HL with microbiological compounds is of particular interest. It was revealed that use of HL in combination with bacterial compound – “Mizorin”, provided a statistically significant yield increase (2 t/ha or 6.6%). At the same time, the plants’ damage by common scab decreased from 0.75 to 0.46 points. The observed effect can be caused by the fact that the beneficial microflora, which is part of the “Mizorin” product, is significantly activated due to the branched matrix of lignin.