Understanding the effectiveness of conservation interventions during times of political instability is important given how much of the world’s biodiversity is concentrated in politically fragile nations. Here, we investigate the effect of a political crisis on the relative performance of community managed forests versus protected areas in terms of reducing deforestation in Madagascar, a biodiversity hotspot. We use remotely sensed data and statistical matching within an event study design to isolate the effect of the crisis and post-crisis period on performance. Annual rates of deforestation accelerated at the end of the crisis and were higher in community forests than in protected areas. After controlling for differences in location and other confounding variables, we find no difference in performance during the crisis, but community-managed forests performed worse in post-crisis years. These findings suggest that, as a political crisis subsides and deforestation pressures intensify, community-based conservation may be less resilient than state protection.