The loss of ecosystem services due to deforestation is of global concern. Financial mechanisms such as REDD+ (reducing emissions from deforestation and forest degradation) have been proposed as ways to support the conservation of tropical forests. Crucial steps in the implementation of REDD+ are to estimate national-level carbon emissions from deforestation and forest degradation and to collect data on local biomass and carbon stocks. In this research, above-ground biomass (AGB) values and associated carbon stocks in a lowland secondary forest are estimated and compared with those in an adjacent primary forest, both growing on limestone in Seram, the Moluccas, Indonesia. Suitable allometric equations for secondary forests in this region and on limestone were not available, so destructive sampling was necessary to determine the AGB in the secondary forest. An allometric equation was developed that makes it possible to estimate the AGB when tree diameter, height and wood density data are available. This biomass estimate was compared with AGB values that were calculated using existing allometric equations for secondary forests. To calculate the biomass and carbon values for the primary forest, an allometric equation from the literature was used. The AGB for trees =10 cm dbh in the secondary forest (140.7 Mg ha–1) was 2.5 times lower than that in the primary forest (349.9 Mg ha–1). Converting these biomass estimates into carbon stocks gave a value of 70.3 Mg ha–1 for the secondary forest and 175.0 Mg ha–1 for the primary forest. The AGB estimate for the secondary forest differs from published values for other areas within the region, because age, type of disturbance and original forest type are non-uniform. The AGB value for the primary forest is comparable to that found in a biomass study conducted in a Malaysian primary limestone forest, but lower than those found in primary forests in Borneo that are dominated by dipterocarps. Ecological limestone studies in the tropics are very rare and more studies of this forest type, and comparisons with adjacent forests on different soil types, are recommended. When the biomass of understory vegetation and other life forms was included, the total AGB in the secondary forest was equal to 176.5 Mg ha–1. As much as 20% of the total AGB was found in life forms other than trees =10 cm dbh. Because secondary forests generally contain many small stems, it is recommended that understory vegetation be included in total AGB estimates for secondary forests. The AGB estimate in the secondary forest varied greatly depending on which of the existing allometric equations was used. Therefore, this study confirms the importance of choosing suitable allometric equations for each forest type and the need to consider destructive sampling when suitable equations are not available. We stress that the allometric equation developed in this study should be used only for old secondary lowland limestone forests in the Moluccas. The fieldwork for this research was carried out in Seram, the Moluccas, Indonesia, from April to June 2011. This research project received financial support from the CoLUPSIA project, Hendrik Muller Fonds and Het Miquel Fonds.