Sustainability of agro-ecosystems can be achieved if farming systems are both ecologically sound and economically viable. Therefore, it is critically important for conservation scientists to see wide-scale biodiversity policy as only one aspect of a complex socio-ecological system, in which independent land managers, subject to financial constraints, make choices subject to a range of objectives, most of which are only tangentially influenced by considerations of nature conservation. Conservation incentives are a policy instrument to reconcile conservation and land managers’ objectives. Two broad approaches – payment for specific conservation actions (payment-for-activities), and payment for specific environmental outcomes (payment-for-results) – warrant particular attention. We investigate how undetected sinks might influence species persistence and richness in different policy and socio-economic contexts. To this end, we used a spatially explicit agent-based model of land use decision making, coupled with a spatially explicit metacommunity model. Our results show that, except when land managers are satisfied by low financial returns, the assumptions made by policy makers regarding habitat suitability of target species can have serious consequences on species’ persistence when sinks are present but not detected. Sinks are more influential for species associated with habitat that does not tend to become rare, due to the profitability associated with land use conversion under free-market conditions. For other habitat types, habitat turnover due to market-driven land use change is more important for conservation.