The study assessed the use of effective microorganisms for the control of apple tree pests. Biological control of phytophagous pests is an environmentally safe alternative to chemical impact on ecosystems. The most successful bioagent used to control insect pests is Bacillus thuringiensis. The objects of research were apple trees of the Jonagold variety. The quantitative composition of the main insect pests of the apple tree by species was determined. The strains of microorganisms were isolated from dead insects of natural populations of leaf-eating phytophagous insects of the orders Coleoptera, Hemiptera, and Lepidoptera. The effectiveness of new bioagents was compared with chemical and biological insecticides in the course of the studies. In the course of studies of the isolated strains, they were found to be able to inhibit the growth of some phytopathogenic fungi. It was shown that the studied strains BT-43, BT-18, and BT-52 have a fungistatic effect, and strain BT-10 has a fungicidal effect against Botrytis cinerea and Alternaria mali Roberts. The effectiveness of the treatment of apple orchards affected by phytophages with bioinsecticides based on selected promising strains of B. thuringiensis was tested. The strain BT-10 proved to be particularly effective against pests, the effect of which is almost equal to or superior to that of deltamethrin. Due to the high efficiency and entomocidal effectiveness against insects of Lepidoptera, it is advisable to use this biological product in the future in the system of control of leaf-eating phytophages. The treatment of apple trees with biological products contributed to a significantly higher yield than the control, which was the highest when treated with the BT-10 strain. Investigating the cost-effectiveness of the used apple protection products based on BT strains, it was shown that treatment with a chemical insecticide reduced the cost by 18% compared to the control. Thus, the research has shown that the treatment of apple plantations with pest and disease control agents is an integral element of the technology of growing and storage of fruits.