Forest soils are important components of the global carbon cycle because they both store and release carbon. Carbon dioxide is released from soil to the atmosphere as a result of plant root and microbial respiration. Additionally, soils in dry forests are often sinks of methane from the atmosphere. Both carbon dioxide and methane are greenhouse gases whose increasing concentration in the atmosphere contributes to climate warming. Thinning treatments are being implemented in ponderosa pine forests across the southwestern United States to restore historic forest structure and reduce the risk of severe wildfire. This study addresses how thinning alters fluxes of carbon dioxide and methane in ponderosa pine forest soils within one year of management and examines mechanisms of change. Carbon dioxide and methane fluxes, soil temperature, soil water content, forest floor mass, root mass, understory plant biomass, and soil microbial biomass carbon were measured before and after the implementation of a thinning and in an unthinned forest. Carbon dioxide efflux from soil decreased as a result of thinning in two of three summer months. Average summer carbon dioxide efflux declined by an average of 34 mg C m−2 hr−1 in the first year after thinning. Methane oxidation did not change in response to thinning. Thinning had no significant short-term effect on total forest floor mass, total root biomass, or microbial biomass carbon in the mineral soil. Understory plant biomass increased after thinning. Thinning increased carbon available for decomposition by killing tree roots, but our results suggest that thinning reduced carbon dioxide emissions from the soil because the reduction in belowground autotrophic respiration was larger than the stimulation of heterotrophic respiration. Methane oxidation was probably not affected by thinning because thinning did not alter the forest floor mass enough to affect methane diffusion from the atmosphere into the soil.