Spatio-temporal summary data of measurements published in Hergoualc'h et al. (2020) Spatial and temporal variability of soil N2O and CH4 fluxes along a degradation gradient in a palm swamp peat forest in the Peruvian Amazon. Global Change Biology X, XX-XX. Data collected in Iquitos, Peru to evaluate the spatio-temporal variability of soil N2O and CH4 fluxes and environmental parameters along a palm swamp peatland degradation gradient (Intact site, moderately degraded site ans heavily degrades site) considering structural changes in vegetation and soil microtography. The supporting information contains a database which presents monthly data averaged by degradation level, M. flexuosa palm status and spatial position. Soil N mineral data (NH4+ and NO3- contents, net mineralization and nitrification rates) was trimonthly collected from October 16 to July 18, and not disaggregated by M. flexuosa palm status.