[1] Management of agricultural soil plays an important role in present and future atmospheric concentrations of the greenhouse gases carbon dioxide (CO₂), nitrous oxide (N₂O), and methane (CH₄). Pesticides are used as management tools in crop production, but little is known about their effects on soil‐atmosphere exchange of CO₂, N₂O, and CH₄. Field studies described in this paper determined the effect of two commonly used fungicides, mancozeb and chlorothalonil, on trace gas exchange. Separate experimental plots, 1 m², were established in nitrogen fertilized no‐tilled native grassland and tilled soils with and without fungicide application. Two studies were conducted. The first study was initiated in June 1999 and lasted for 1 year with monthly flux measurements from tilled and no‐till soils. The second study commenced in August 2001 with twelve weekly measurements from tilled soils only. From both studies mancozeb suppressed emissions of CO₂ and N₂O in the tilled soil by an average of 28% and 47%, respectively. This suppression corresponded with efficacy periods of 14–29 and 56–77 days, respectively. From the no‐till soils mancozeb decreased CO₂ and N₂O emissions by 33% and 80% for periods of 29 and 94 days, respectively. Mancozeb inhibited CH₄ consumption in the first study by 46% and 71% in the tilled and no‐till soil for periods of 8 and 29 days, respectively, but had no effect in the second study. From both studies chlorothalonil initially suppressed CO₂ and N₂O emissions and enhanced CH₄ uptake in the tilled soil by an average of 37%, 40%, and 115%, respectively. These effects corresponded with efficacy periods of 14–29, 21–56, and 1–14 days, respectively. In the no‐till soil chlorothalonil inhibited CO₂ and N₂O emissions and enhanced CH₄ uptake by 29%, 48%, and 86% for periods of 29, 56, and 56 days, respectively. Following the initial period of suppression, chlorothalonil subsequently enhanced N₂O emissions in the tilled soil by an average of 51% and in the no‐till soil by 81% before returning to near background levels. The beginning of increased N₂O emissions from the chlorothalonil‐amended plots corresponded with a maximum soil concentration of the chlorothalonil degradate, 4‐hydroxy‐2, 5, 6‐trichloroisophthalonitrile. The site specific global warming potential (GWP) resulting from the fluxes of CO₂, N₂O, and CH₄ from all soils was determined to decrease by an average 26% and 21% as a result of a single application of mancozeb or chlorothalonil, respectively. The decrease in CO₂ emissions in the fungicide‐amended plots potentially could result in the conservation of as much as 1200 and 2400 kg C ha⁻¹yr⁻¹ organic carbon in the tilled and no‐till plots, respectively. Therefore it is feasible that application of certain fungicides to agricultural soil might lead to enhanced soil carbon sequestration and thus have additional positive effects on atmospheric CO₂concentrations.