Spatio-temporal summary data of measurements published in Hergoualc'h et al. (2022) Major CO2 losses from degradation of Mauritia flexuosa peat swamp forests in western Amazonia. Global Change Biology X, XX-XX. Data collected in Iquitos, Peru to evaluate the spatio-temporal variability of total soil respiration (Rs-CO2), heterotrophic soil respiration (Rh-CO2), environmental parameters, litterfall and leaf decomposition along a palm swamp peatland degradation gradient (Intact site, moderately degraded site and heavily degraded site). Soil respiration and environmental parameters were measured considering structural changes in vegetation and soil microtography. The supporting information contains three databases. The first one presents monthly soil respiration and environmental variables 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 2016 to July 2018, and not disaggregated by M. flexuosa palm status. The second database contains monthly averaged litterfall data which was collected from June 2014 to July 2018. The third database contains averaged litter decomposition data which was studied from July 2015 to January 2017