Rubber agroforests in the mostly deforested lowlands of Sumatra, Indonesia are threatened by conversion into monoculture rubber or oil palm plantations. We applied an agent-based model to explore the potential effectiveness of a payment for ecosystem services (PES) design through a biodiversity rich rubber eco-certification scheme. We integrated conditionality, where compliance with biodiversity performance indicators is prerequisite for awarding incentives. We compared a PES policy scenario to ‘business-as-usual’ and ‘subsidized land use change’ scenarios to explore potential trade-offs between ecosystem services delivery and rural income. Results indicated that a rubber agroforest eco-certification scheme could reduce carbon emissions and species loss better than alternative scenarios. However, the suggested premiums were too low to compete with income from other land uses. Nevertheless, integrating our understanding of household agent behavior through a spatially explicit and agent-specific assessment of the trade-offs can help refine the design of conservation initiatives such as PES.