In a changing global environment, with increasing pressure on ecosystem goods and services, biodiversity conservation is likely to become increasingly important. However, with the current global financial crisis, governments are increasingly trying to stabilise economies through spending cuts aiming to reduce national deficits. Within such an economic climate, the devolution of governance through public participation is an intrinsically appealing concept. We outline a number of challenges that explain why increased participation in biodiversity management has been and may continue to be problematic. Using as a case study the local stakeholder-driven Moray Firth Seal Management Plan in Scotland, we identify four key conditions that were crucial to the successful participatory management of a biodiversity conflict: a local champion, the emergence of a crisis point, the involvement of decision-makers, and long-term financial and institutional support. Three of the four conditions point to the role of direct government involvement, highlighting the risk of devolving responsibility for biodiversity conflict management to local communities. We argue that without an informed debate, the move towards a more participatory approach could pose a danger to hard-won policy gains in relation to public participation, biodiversity conservation and conflict management.