N2O, CH4 and CO2 soil-atmosphere exchange and controlling environmental factors were studied for a 3-month period (dry-wet season transition) at the Kakamega Rain forest, Kenya, Africa, using an automated measurement system. The mean N2O emission was 42.9 ± 0.7 μg N m−2 h−1 (range: 1.1–324.8 μg N m−2 h−1). Considering the duration of dry and wet season the annual N2O emission was estimated at 2.6 ± 1.2 kg N ha−1 yr−1. Large pulse emissions of N2O were observed after the first rainfall events of the wet season, and the magnitude of N2O emissions steadily declined thereafter. A comparable trend in soil CO2 emissions (mean: 71.8 ± 0.3 mg C m−2 h−1) indicates that the rapid mineralization of litter accumulated during the dry period produced the high N2O emissions at the start of the wet season. Manual N2O emission measurements at four additional rain forest sites were comparable to those measured at the main site, whereas N2O emissions measured at a regrowth site were significantly lower. Spatial differences in N2O emissions could be explained by differences in soil texture and topsoil C:N-ratio (CO2: subsoil C and N concentrations), whereas the temporal variability of N2O and CO2 emissions was primarily driven by soil moisture. Soils predominantly acted as sinks for CH4 (−56.4 ± 0.8 μg C m−2 h−1). For some chamber positions, episodes of net CH4 release were observed, which could be due to high WFPS and/or termite activity. CH4 fluxes were weakly correlated with soil moisture levels but showed no relation to temperature, texture, pH, carbon or nitrogen contents.