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Pesticides are biologically active compounds and their application may alter soil microbial communities and thus could possibly impact greenhouse gas (GHG) emissions. However, this aspect of agricultural production is rarely studied at the field scale. To address this knowledge gap, we conducted a 2-year field study growing maize (corn) under three pesticide application levels (no, medium, and high) in two agricultural practices: bare soil (conventional) and using cereal rye as a cover crop. In plots with no pesticide inputs, weeds were managed through hand removal weekly. We quantified GHG emissions, changes in soil labile carbon (C), nitrogen (N), and other typical growth parameters in the Iron Horse Farm, Georgia. Corn grain yields were within 93% of the estimated site yield potential, with yield significantly higher in 2021 than in 2022. Using a linear mixed model, including the data in both 2021 and 2022 for soil nutrients, soil temperature, soil moisture, agricultural practice, and pesticide levels as fixed effects and date and plot as random effects, soil surface carbon dioxide (CO2) fluxes were statistically significantly associated with soil temperature and soil moisture. Soil N2O emissions were only associated with soil moisture. Soils in general served as a sink for CH4 in all the agricultural practices and soil CH4 fluxes were also only associated with soil moisture. Three plots with high soil C/N ratio with a visible presence of biochar resulted in several high CH4 flux events during the growing season. Soils from all plots were net sources of GHG and there were no significant differences in the amount of soil C sequestered between the plots. Our study shows that none of the variables we analyzed - yield, individual/net GHG emissions or the amount of C sequestered - in the two years of our experiment were impacted by the magnitude of pesticide application. However, this may change in a long-term experiment. Further research is essential to understand the underlying mechanism for high CH4 pulses in corn fields with high C/N ratio, as positive impacts of biochar might coincide with large negative consequences on climate, depending on conditions.