Technical Abstract: Carbon dioxide (CO2) and methane (CH4) are two gases most responsible for contemporary increases in the radiative forcing of the atmosphere. Fluxes of both gases are affected by agriculture. Soil comprises the largest terrestrial reservoir of carbon, which is oxidized to CO2 upon agricultural conversion. Agriculture also diminishes methane oxidation in arable soils – Earth’s largest biological sink for atmospheric CH4. We examined relationships between soil microbial diversity and the magnitude and stability of CO2 production and CH4 oxidation by conducting molecular surveys of methane–oxidizing bacteria (methanotrophs) and total bacterial diversity and measuring gas fluxes across a range of land uses at a site in the upper U.S. Midwest. We found a 7-fold reduction and increased variability in methane consumption in agricultural sites compared to deciduous forest sites, as well as a proportionate decrease in methanotroph diversity. In fields abandoned from agriculture, the rate and stability of methane consumption, along with the diversity of methanotrophs, increased with time since abandonment. Conversely, estimates of total bacterial diversity in soil were not related to the rate or stability of CO2 emission. Our results are consistent with the hypothesis that microbial diversity is a strong predictor of the magnitude and variability of processes catalyzed by organisms with highly specialized metabolisms such as methane oxidation, and a poor predictor of processes driven by widely distributed metabolic processes like carbon dioxide production. The data also suggest that managing lands to conserve or restore methanotroph diversity could mitigate the atmospheric concentrations of this potent greenhouse gas.