We compared seven scenarios for selecting incentive proposals, and evaluated their contribution to regional conservation outcomes. Scenarios ranged from strategic site assessment where proposals were ranked on scores from site-scale data and a priori regional value to systematic regional assessment with selection of proposals using optimization algorithms. The selection scenarios were simulated using proposals from a conservation investment program in South-eastern Australia. All selection scenarios provided a positive gain in biodiversity compared with selecting no proposals. Regional assessments provided ∼4% gain in the biodiversity index over site assessments. The performance of scenarios using optimization was similar to scenarios using rankings. A framework for integrating site and regional approaches for selecting proposals for conservation management is proposed, where proposals are assessed on their contribution to regional biodiversity outcomes rather than just on the comparative gain in biodiversity at the site, and regional conservation priorities are updated between rounds of incentive programs.