AbstractNatural forests in South‐East Asia have been extensively converted into other land‐use systems in the past decades and still show high deforestation rates. Historically, lowland forests have been converted into rubber forests, but more recently, the dominant conversion is into oil palm plantations. While it is expected that the large‐scale conversion has strong effects on the carbon cycle, detailed studies quantifying carbon pools and total net primary production (NPPtotal) in above‐ and belowground tree biomass in land‐use systems replacing rainforest (incl. oil palm plantations) are rare so far. We measured above‐ and belowground carbon pools in tree biomass together with NPPtotal in natural old‐growth forests, ‘jungle rubber’ agroforests under natural tree cover, and rubber and oil palm monocultures in Sumatra. In total, 32 stands (eight plot replicates per land‐use system) were studied in two different regions. Total tree biomass in the natural forest (mean: 384 Mg ha−1) was more than two times higher than in jungle rubber stands (147 Mg ha−1) and >four times higher than in monoculture rubber and oil palm plantations (78 and 50 Mg ha−1). NPPtotal was higher in the natural forest (24 Mg ha−1 yr−1) than in the rubber systems (20 and 15 Mg ha−1 yr−1), but was highest in the oil palm system (33 Mg ha−1 yr−1) due to very high fruit production (15–20 Mg ha−1 yr−1). NPPtotal was dominated in all systems by aboveground production, but belowground productivity was significantly higher in the natural forest and jungle rubber than in plantations. We conclude that conversion of natural lowland forest into different agricultural systems leads to a strong reduction not only in the biomass carbon pool (up to 166 Mg C ha−1) but also in carbon sequestration as carbon residence time (i.e. biomass‐C:NPP‐C) was 3–10 times higher in the natural forest than in rubber and oil palm plantations.