Nowadays, chemical pesticides are the most widespread measure used to control crop pests and diseases. However, their negative side effects prompted the researchers to search for alternative options that were safer for the environment and people. Pesticide biodegradation by microorganisms seems to be the most reasonable alternative. The aim of the laboratory studies was to assess the influence of Bacillus subtilis and Trichoderma harzianum, used separately and combined together, on fluopyram and tebuconazole degradation. In field studies, the degradation of fluopyram and tebuconazole after the application of the biological preparation in apples was investigated. The results from the laboratory studies show that the greatest decomposition of fluopyram and tebuconazole was observed in tests with T. harzianum in a range of 74.3–81.5% and 44.5–49.2%, respectively. The effectiveness of fluopyram degradation by B. subtilis was 7.5%, while tebuconazole inhibited bacterial cell growth and no degradation was observed. The mixture of microorganisms affected the degradation of fluopyram in a range of 8.3–24.1% and tebuconazole in a range of 6.1–23.3%. The results from the field studies show that degradation increased from 3.1 to 30.8% for fluopyram and from 0.4 to 14.3% for tebuconazole when compared to control samples. The first-order kinetics models were used to simulate the residue dissipation in apples. For the determination of pesticide residues, the QuEChERS method for apple sample preparation was performed, followed by GC–MS/MS technique. Immediately after the treatments, the maximum residue level (MRL) values for tebuconazole were exceeded, and it was equal to 100.7% MRL for the Red Jonaprince variety and 132.3% MRL for the Gala variety. Thus, preharvest time is recommended to obtain apples in which the concentration of pesticides is below the MRL and which can be recognized as safe for humans.