Despite the growing ecological and social importance of second-growth and regenerating forests across much of the world, significant inconsistencies remain in the legal framework governing these forests in many tropical countries and elsewhere. Such inconsistencies and uncertainties undermine attempts to improve both the transparency and sustainability of management regimes. Here, we present a case-study overview of some of the main challenges facing the governance of second-growth forests and the forest restoration process in the Brazilian Amazon, with a focus on the state of Pará, which is both the most populous state in the Amazon and the state with the highest rates of deforestation in recent years. First, we briefly review the history of environmental governance in Brazil that has led to the current system of legislation governing second-growth forests and the forest restoration process in Pará. Next, we draw on this review to examine the kinds of legislative and operational impediments that stand in the way of the development and implementation of a more effective governance system. In particular, we highlight problems created by significant ambiguities in legal terminology and inconsistencies in guidance given across different levels of government. We also outline some persistent problems with the implementation of legal guidance, including the need to understand local biophysical factors in order to guide an effective restoration program, as well as difficulties presented by access to technical assistance, institutional support and financial resources for the establishment and monitoring of both existing secondary forests and newly regenerating areas of forest. Whilst we focus here on a Brazilian case study, we suggest that these kinds of impediments to the good governance of second-growth forests are commonplace and require more concerted attention from researchers, managers and policy makers.