Large areas of Indonesian peatlands have been converted for agricultural and plantation forest purposes. This requires draining with associated CO2 emissions and fire risks. In order to identify alternative management regimes for peatlands, it is important to understand the sustainability of different peatland uses as well as the economic benefits peatlands supply under different land uses. This study explores the key sustainability issues in Indonesian peatlands, the ecosystem services supplied by peatlands, and potential responses to promote more sustainable peatland use. A literature review and spatial analysis were conducted. Based on predominantly government data, we estimate the amount of Indonesian peatlands that has been converted between 2000 and 2014. We quantify increases in oil palm and plantation forest crop production in this period, and we analyse key sustainability issues, i.e. peat fires and smoke-haze, soil subsidence and flood risk, CO2 emissions, loss of habitat (in protected areas), and social conflicts that influence sustainability of Indonesian peatlands management. Among others we show that CO2 emissions from peatlands in Indonesia can be estimated at between 350 and 400 million ton CO2 per year, and that encroachment of oil palm and plantation forestry (acacia, rubber) has taken place on 28% of protected areas. However, as we examine, the uncertainties involved are substantial. Based on our findings, we distil several implications for the management of the peatlands. © 2017, The Author(s).