The worldwide implementation of Marine Protected Areas (MPAs) has been used as a conservation measure to preserve marine biodiversity. Due to technological limitations, many early designated MPAs often neglected the distribution of marine habitats. Marine remote-sensing techniques development represents an opportunity to reshape and rethink MPA designs. This study focuses on the Vila Franca do Campo MPA (established in 1983) on São Miguel Island, Azores, using advanced acoustic remote-sensing techniques (MBES, SSS). Mapping of approximately 394 ha revealed a 1–3 ratio between rock and sediment habitats within the MPA, while the adjacent unprotected area showed a ratio of less than 1–2, with significant black coral gardens observed below 40 m depth. According to these results and the ecological importance of the organisms detected, we recommend remodeling the MPA. Furthermore, identifying readily accessible black coral communities provides an opportunity for comprehensive assessments of their contribution to marine biodiversity and conservation resources. •Remote sensing tools such as MBES, SSS allow the creation of accurate habitat maps.•Shallower black coral gardens were identified beyond the MPA boundaries.•Habitats discovered are of global conservation concern and suggest MPA restructuring.•Several MPAs have deficient ecological assessments due to lack of ecosystem approach.