Scale mismatches between the spatial scales of human decision-making and natural processes produce environmental problems such as global warming and losses of biodiversity. The damages caused by the scale mismatches can be avoided by payment for ecological services from those who suffer from the damages to providers of these services. This paper presents a spatially explicit land-use model to investigate the consequences of scale mismatches for pollination and carbon storage services and examine the effect of payment for only carbon storage services. The model integrates processes in multiple spatial scales ranging from the parcel level used by landowners’ decision about deforestation, to the larger scale used by bees to pollinate plants, and finally to the global scale where global warming damages emerge. We show that payment for carbon storage services may become an effective mechanism to protect forests. However the damage of pollination services and payment of carbon storage services at different special scales can result in a creation of inequity among landowners in income level. These findings suggest that market-based approaches that focus on conservation of a single ecosystem service may reproduce unequal power relations among landowners.