Protected areas (PAs) are our principal conservation strategy and are evolving rapidly, but we know little about the real-world management and governance of new forms. We review the evolution of Madagascar's PA system from 2003 to 2016 based on our experience as practitioners involved. During this period PA coverage quadrupled and the network of strict, centrally-governed protected areas expanded to include sites characterized by: i) multiple-use management models in which sustainable extractive natural resource uses are permitted, ii) shared governance arrangements involving non-governmental organizations (NGOs) and local community associations, and iii) a management emphasis on livelihood-based approaches and social safeguards. We discuss the principal challenges for the effectiveness of the expanded system and detail management/policy responses. These include i) enhancing stakeholder participation, ii) ensuring financial sustainability, iii) enforcing rules, iv) ensuring the ecological sustainability of PAs faced with permitted resource extraction, v) reducing the natural resource dependence of local communities through transformative livelihood change, and vi) developing longterm visions to reconcile the differing objectives of conservation NGOs and other stakeholders. In general PAs have had limited effectiveness in reducing deforestation and other threats, which may be related to their rapid establishment processes and the complexity of management towards multiple objectives, coupled with insufficient resources. While Madagascar's achievements provide a basis for conserving the country's biodiversity, the challenge faced by its protected areas will continue to grow.