Large-scale disturbances and local stressors, most notably bleaching events, sedimentation, and overfishing, impact coral reefs around Madagascar. To enhance reef resilience, managers have established several marine protected areas (MPAs) since 1966. Here, we assess the effects of MPAs on the resilience potential of coral reefs using a multi-factor Recovery Index (RI), based on a multi-criteria analysis: the Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS). We sampled 18 stations, half of which in unfished areas, along three regions (Masoala in the NE, Nosy-Be in the NW and Salary Nord in the SW) that have been affected by the bleaching event of 2016, the most recent large-scale disturbance. We found a marked variation in RI between regions, with Masoala having the highest RI. We suggest that these results relate to the lower frequency of sea surface temperature anomalies (SSTa) along the east coast and the combination of more frequent SSTa and higher anthropogenic pressures on the west coast. We also found RI variation among stations; most stations with higher RI have high juvenile coral densities, which support important coral replenishment capacities. We further noted a positive effect of MPAs on recovery potential at Nosy-Be. We argue that the effectiveness of MPAs in Madagascar can be increased with Locally Managed Marine Areas, which feature a strong involvement of intended users and are often easier to manage. Our study also demonstrates that TOPSIS can be a useful tool to estimate the recovery capacities of coral assemblages and to support resilience-based conservation actions.