The object of research was the soil from an orchard after 27 years of apple cultivation, showing signs of fatigue resulting in weaker growth of apple seedlings planted into it, and the soil sampled on the same farm, but not used for growing fruit trees. The physicochemical properties of both soils did not differ significantly. In sick soil, no pathogens of fungal or fungi-like origin were found, and the number of nematodes was below the threshold of economic threat. There is a suspicion that abiotic factors could be responsible for soil fatigue. It has been demonstrated that the cultivation of spring and winter wheat, triticale and white mustard before planting apple ‘Antonovka’ seedlings, had a positive impact on their growth. The best effect was obtained after the cultivation of white mustard or after the introduction of mustard seed meal into the soil, which was also confirmed by measurements of the intensity of apple seedlings photosynthesis. The cultivation of these phytosanitary plants or the addition of mustard seed meal positively influenced the biological potential of the soil expressed by a significant increase in the population of bacteria from the genera Pseudomonas and Bacillus. There was also a very large increase in the number of Trichoderma spp. fungi after the addition of mustard seed meal into the soil and winter wheat cultivation.