The effect of beneficial soil fungi, bacteria and mineral fertilizers containing nitrogen, phosphorus and potassium on the level and species composition of weed infestation, uptake of macronutrients by weeds and the nutritional status of ‘Sampion’ apple trees with nitrogen (N), phosphorus (P), potassium (K), magnesium (Mg) and calcium (Ca) was assessed in three-year studies. In the field experiment, the effect of thirteen treatments was investigated, where fungal or bacterial inocula and mineral fertilizers at a standard dose and a dose reduced by 40% were applied individually or together. The fungal inoculum contained two species: Aspergillus niger and Purpureocillium lilacinum. The bacterial consortium consisted of three Bacillus strains: Bacillus sp., Bacillus amyloliquefaciens and Paenibacillus polymyxa. The weight of weeds and the uptake of macronutrients by weeds in the apple orchard increased significantly more after the application of mineral fertilization than after the application of beneficial organisms. The increased uptake of macronutrients by weeds did not significantly change the mineral nutritional status of apple trees expressed as the content of N, P, K Mg and Ca in apple leaves. After the use of NPK mineral fertilization, also with the addition of beneficial organisms, the uptake of N by both weeds and apple trees increased. P and K were more efficiently absorbed by weeds and they achieved greater benefits from fertilization with these two macroelements than trees.