Progressive conversion of tropical rainforests to agricultural monocultures in South East Asia increasingly affects landscape types such as riparian areas. The impacts of conversions on soil organic matter (SOM) vary with changing landforms. However, this was often not accounted for in previous studies where SOM in soils in riparian areas was combined with SOM from well-drained adjacent slopes. Because riparian areas have a high carbon (C) storage potential, our objectives were i) to assess their C stocks after conversion to rubber and oil palm plantations in Sumatra (Indonesia) and ii) to compare the impacts of land use conversion on C stocks between riparian and well-drained areas. Average soil C stock losses from the top 30 cm were about 14% and 4% following conversion of riparian forest to rubber and oil palm plantations, respectively, indicating a high resistance of C to mineralization. C losses from well-drained areas were twice as high as from riparian areas after the respective conversion. δ13C values from riparian areas showed clear heterogeneity down soil profiles that was explained i) by alternating oxic and anoxic conditions, leading to reduced SOM and litter decomposition in riparian areas and ii) by mineral sediments and organic matter deposition and accumulation by erosion from adjacent slopes covered by plantations. We conclude that riparian areas are more resilient in terms of soil C storage towards land-use change than well-drained areas because of sediment deposition and reduced oxygen availability. On this basis, we developed a conceptual model of the effects of land-use change and various ecotone characteristics on SOM mineralization in the top- and subsoil of riparian areas.