Boundary organizations have been promoted as a measure to improve the effectiveness of conservation efforts by building stronger relationships between scientists, policy makers, industry and practitioners (Cook et al. 2013). While their promise has been discussed in theory, the work of and expectations for boundary organizations are less defined in practice. Biodiversity conservation is characterized by complexity, uncertainty, dissent and tight budgets, so boundary organizations face the challenging task of demonstrating their value to diverse stakeholders. This paper examines the challenges that boundary organizations face when seeking to evaluate their work. While no ‘off-the-shelf' solution is available for a given boundary organization, many lessons can be learned from the evaluation literature. This paper synthesizes key areas of decision making to underpin the choice of evaluation approaches.