This paper addresses the question of legitimacy in REDD? governance in Indonesia. It develops a legitimacy framework that builds on elements of Scharpf (J Eur Pub Policy 4(1):18-36, 1997) input and output legitimacy concept and the political economy lens described by Brockhaus and Angelsen (Analysing REDD?: Challenges and choices, CIFOR, Bogor, 2012). Using data collected through key informant interviews and focus groups, we identify and explore stakeholder perceptions of legitimacy. The analysis reveals a complex interplay between input and output legitimacy, finding that state, nonstate and hybrid actors perceive output legitimacy (i.e. project outcomes) as highly dependent on the level of input legitimacy achieved during the governance process. Nonstate actors perceive proxies for input legitimacy, such as participation and inclusion of local people, as goals in themselves. In the main, they perceive inclusion to be integral to the empowerment of local people. They perceive output legitimacy as less important because of the intangibility of REDD? outcomes at this stage in the process. The findings also highlight the challenges associated with measuring the legitimacy of REDD? governance in Indonesia.