Soybean is a legume of high economic value, valued primarily for the high protein and oil content in its seed. Due to the advisability of seeking optimal solutions in the agronomy of this valuable legume, a study was undertaken to determine the effect of different fertilisation methods using preparations containing effective microorganisms (EM) on yield, content of some seed quality components and nodule formation of soybean. The experiment was set up in a randomised block design in three replicates, on plots with an area of 20 m2. The soybean cultivar ‘Merlin’ was grown. It was shown that application of mineral fertilisation supplemented with EM spraying was the most beneficial for soybean yield, followed by NPK fertilisation alone. All fertilisation treatments had a beneficial effect on protein content in soybean seed, compared to the control treatment. An opposite relationship was found in the case of the percentage oil content. The highest number and weight of nodules on soybean roots were noted in the treatment with EM spraying three times.