This dataset contains terrestrial fluxes of nitrous oxide (N2O), methane (CH4) and ecosystem respiration (carbon dioxide (CO2)) calculated from static chamber measurements in mature oil palm plantations on mineral soil, managed by Sinar Mas Agro Resources and Technology Research Institute (SMARTRI) and located on the Ujung Tanjung Estate in Riau, Sumatra, Indonesia. Measurements were made monthly, from October 2018 until September 2019. A total of 54 static chambers were installed across nine plots, representing three different understory vegetation treatments: normal complexity (an intermediate-level of understory spraying with herbicide); reduced complexity (spraying of all understory vegetation with herbicides); and enhanced complexity (no herbicide spraying and limited understory cutting). Six chambers were installed in each of the nine plots, resulting in 18 replicates of each treatment. In addition, soil moisture measurements were also taken around each chamber. The dataset was associated with a foreign research permit, issued by Foreign Research Permit Division Ministry of Research and Technology/National Research and Innovation Agency, Indonesia. As the project spanned two years it was covered by two permits, RISTEK permit number: 323/SIP/FRP/E5/Dit.KI/X/2018 and RISTEK permit number: 8B/TKPIPA/E5/Dit.KI/VIII/2019. Full details about this dataset can be found at https://doi.org/10.5285/378f028d-ab04-4fa5-a5ca-61f78ea0adb0