Ecosystems are increasingly disturbed by natural disturbances and human stressors. Understanding how a disturbance can propagate through an entire ecosystem and how induced changes can last after apparent recovery is key to guide management and ecosystem restoration strategies. Monitoring programs and impact assessment studies rely mostly on indicators based only on species relative abundance and biomass, potentially misinforming management efforts. Impacts on ecosystem structure and functioning, and subsequent delivery of ecosystem services, are too often overlooked. Here we use an ecosystem network approach to assess the recovery pathway and potential recovery debts of a coral reef ecosystem, following a pulse disturbance. We show that although species abundance and biomass indicators recovered in a decade after the perturbation, the ecosystem as a whole presented a recovery debt. The ecosystem structure lost complexity (became ‘‘food chain like’’) and lost about 29% of its overall cycling efficiency and 9% of its transfer efficiency. Although the ecosystem trophic network in the fore reef may have maintained its general functioning, the ecosystem network in the lagoon, not directly exposed to the disturbance, presented a stronger recovery debt. Our results give new insights on how ecosystem network approaches can help identify ecosystem impacts and recovery pathways.