Modern approaches to optimising the nutrition of vegetable plants often have low efficiency and negatively affect various components of the agrobiocoenosis (soil, microbiota). In this regard, the purpose of the study was to determine the influence of various fertiliser systems on the yield and quality of onions in irrigated vegetable-fodder crop rotation, changes in the main agrochemical and microbiological parameters of the soil. The study was conducted in the laboratory of agrochemical research and quality of products of the Institute of Vegetable and Melon Growing of NAAS of Ukraine. Research methods: long-term stationary field experiment; laboratory determination of agrochemical and microbiological parameters of soil and biochemical composition of bulbs; statistical data processing. It is determined that a significant increase in the content of nitrate nitrogen in the arable soil layer is provided by the use of mineral fertilisers, mobile compounds of phosphorus and potassium – mineral and systems. The use of mineral fertilisers leads to an increase in the number of fungi in the soil rhizosphere and a decrease in the potential activity of nitrogen fixation, which worsens the microbiological activity of the soil. The application of organic fertilisers in combination with mineral fertilisers leads to an increase in the number of nitrogen-fixing microorganisms and potential nitrogen-fixing activity, which improves soil fertility. The use of organo-mineral and mineral fertiliser systems leads to an increase in the yield of onions by 6.6-8.6 t/ha or 41.3-53.8%. When using biologised nutrition optimisation systems, the yield increases by 19.4-23.8%. The maximum level of onion yield is indicated for the introduction of organo-mineral fertiliser systems(63 t/ha of humus + randomly N45P45K45; 36 t/ha of humus + locally N45P45K45); causing an increase in yield by 8.2-8.6 t/ha.There is a certain pattern of a decrease in the dry matter content in bulbs and an increase in the nitrate content undervarious fertiliser systems. The research materials are of practical value for the implementation of nutrition optimisationsystems aimed at both sustainable growth in the yield of vegetable products and maintaining the level of soil fertilityof vegetable agrobiocoenoses