Pesticides are widely used in conventional agriculture, either applied separately or in combination during the culture cycle. Due to their occurrence and persistence in soils, pesticide residues may have an impact on soil microbial communities and on supported ecosystem services. In this regard, the EFSA (European Food Safety Authority) recently published a scientific opinion inciting to change pesticide risk assessment to better protect soil microbe-mediated processes. Climate change is another major concern for all living organisms including soil microbial community stability. Extreme climatic events, such as heat waves or heavy rainfalls, are becoming more and more frequent and their impact on soil microbial diversity and functions have already been demonstrated. The objectives of this study were to evaluate the effects of temperature and humidity disturbances and pesticide active ingredients exposure on soil microbial community structure and functions. To this end, 250 soil microcosms were exposed to either a heat disturbance, a high humidity to mimic heavy rain, or no environmental disturbance. After three days of recovery, soil microcosms were treated with different active ingredients: clopyralid (herbicide), cypermethrin (insecticide) and pyraclostrobin (fungicide). The treatments were applied alone or in combination at 1x or 10x of the agronomical dose. We then evaluated the effects of the disturbances and the active ingredients on various microbial endpoints related to the diversity and the structure of soil microbial communities, and with a specific focus on microbial guilds involved in nitrification. Overall, we demonstrated that the impact of environmental disturbances applied to soil microcosms, especially heat, on microbial endpoints was stronger than that of the active ingredients applied alone or in combinations. Compounded effects of environmental disturbances and active ingredients were detected, but sparsely and were of small scale for the chosen pesticides.