We investigated changes in soil-atmosphere flux of CH4, N2O, and NO resulting from the succession of pasture to forest in the Atlantic lowlands of Costa Rica. We studied a dozen sites intensively for over one year in order to measure rates and to understand controlling mechanisms for gas exchange. CH4 flux was controlled primarily by soil moisture content. Soil consumption of atmospheric CH4 was greatest when soils were relatively dry. Forest soils consumed CH4 while pasture soils which had poor drainage generally produced CH4. The seasonal pattern of N2O emissions from forest soils was related exponentially to soil water-filled pore space. Annual average N2O emissions correlated with soil exchangeable NO3− concentrations. Soil-atmosphere NO flux was greatest when soils were relatively dry. We found the largest NO emissions from abandoned pasture sites. Combining these data with those from another study in the Atlantic lowlands of Costa Rica that focused on deforestation, we present a 50-year chronosequence of trace gas emissions that extends from natural conditions, through disturbance and natural recovery. The soil-atmosphere fluxes of CH4 and N2O and of NO may be restored to predisturbance rates during secondary succession. The changes in trace gas emissions following deforestation, through pasture use and secondary succession, may be explained conceptually through reference to two major controlling factors, nitrogen availability and soil-atmosphere diffusive exchange of gases as it is influenced by soil moisture content and soil compaction.