To accurately quantify tropical peatlands’ contribution to global greenhouse gas emissions, and to understand how emissions from peat may change in the future, long-term measurements over seasons and years are needed. Sampling soil respiration over a range of temperature and moisture conditions in the field is valuable for understanding how peat soil emissions may respond to climate change. We collected monthly measurements of total soil respiration, moisture and temperature from forest and smallholder oil palm plantations on peat in Central Kalimantan, Indonesia. Our study period, from January 2014 through September 2015, covered wet–dry transitions during 1 year with relatively normal precipitation and one El Niño year. Oil palm plots, with lower water table, had 22% higher total soil respiration (0.71 ± 0.04 g CO2 m-2 h-1) than forest plots (0.58 ± 0.04 g CO2 m-2 h-1) over the entire monitoring period. However, during the El Niño event in September 2015, despite overall lower water table levels in oil palm plots, total soil respiration was higher in forest (1.24 ± 0.20 g CO2 m-2 h-1) than in oil palm (0.90 ± 0.09 g CO2 m-2 h-1). Land-use change continues to be an important driver of carbon dioxide (CO2) emissions from Indonesian peatlands. However, the stronger response of total soil respiration to extreme drought in forest indicates the potential importance of climate regime in determining future net carbon (C) emissions from these ecosystems. Future warming and increased intensity of seasonal drying may increase C emissions from Indonesian peatlands, regardless of land-use.