Secondary tropical forests are at the forefront of deforestation pressures. They store large amounts of carbon, which, if compensated for to avoid net emissions associated with conversion to non-forest uses, may help advance tropical forest conservation. We measured above- and below-ground carbon stocks down to 1 m soil depth across a secondary forest and in oil palm plantations in Malaysia. We calculated net carbon losses when converting secondary forests to oil palm plantations and estimated payments to avoid net emissions arising from land conversion to a 22-year oil palm rotation, based on land opportunity costs per hectare. We explored how estimates would vary between forests by also extracting carbon stock data for primary forest from the literature. When tree and soil carbon was accounted for, payments of US$18-51 tCO2-1 for secondary forests and US$14-40 tCO2-1 for primary forest would equal opportunity costs associated with oil palm plantations per hectare. If detailed assessments of soil carbon were not accounted for, payments to offset opportunity costs would need to be considerably higher for secondary forests (US$28-80 tCO2-1). These results show that assessment of carbon stocks down to 1 m soil depth in tropical forests can substantially influence the estimated value of avoided-emission payments.