This study aimed to evaluate the effects of pesticides from different origins on several bacteria in the microbiota of Bombus terrestris. In the experiments, recommended field doses (1/1) and sublethal doses (1/10, 1/100, 1/1000) of Subtilex Foliar (Bacillus subtilis MBI 600, Bioglobal©) and Pusula (Thiamethoxam, Hektaş©) were used. The experiments were performed with 5 replications (10 worker bees per replication). The worker bees were fed the sugar syrup + pesticide mixture prepared for 5 days in each replication. On the fifth day after applications, 5 random individuals from each trial were selected from the live worker bees and, after being mechanically euthanized, placed in sterilized falcon tubes labeled with experimental group details. The same procedure was applied to the microbiota analysis of the control group as the experimental groups. These individuals were then analyzed to determine microorganism changes. According to the results obtained, the colony development of two different species of bacteria, Staphylococcus xylosus and S. gallinarum, was determined in the control group. Staphylococcus xylosus and S. gallinarum were completely inhibited in 1/1 and 1/10 dose applications of B. subtilis MBI 600, while the dominant species was B. subtilis MBI 600. Staphylococcus xylosus in the control group became dominant after the application of 1/100 dose of B. subtilis MBI 600, and after the application of 1/1000 dose, B. subtilis MBI 600 could not colonize. When Thiamethoxam applications were compared with the control group, Staphylococcus gallinarum colonies and Pseudomonas sp. colonies became dominant in individuals who received 1/1 dose application. The results show that the different origins of the pesticides used cause significant changes in the microbiota of worker bees for life.