In this paper, the physiography, geomorphological features, and sedimentary bedforms of the offshore Egadi Islands (Italy) have been illustrated and mapped through an integrated analysis of high-resolution bathymetric, seismo-acoustic, and sedimentological data. The study area is characterized by a wide, up to 25 km, continental shelf which is separated by a NNW-trending linear incision, the Marettimo Channel, along which several erosional and depositional features have been detected and mapped. Sedimentary prograding wedges were detected at water depths between 100–125 m along the shelf margin, which accumulated during the sea-level fall and lowstand stages of the last glacio-eustatic cycle (post- MIS 5.5). This study detected several slope breaks defining scarps across the continental shelf, which were interpreted as coastal cliffs that originated during the post-LGM eustatic sea-level rise. Several fields of different types of sedimentary bedforms, including 2-D and 3-D hydraulic dunes and sorted bedforms, were found across the continental shelf, providing evidence of a high hydrodynamic regime affecting the seafloor. Further on, this study recognized erosive and depositional features related to bottom currents (contourites) in the Marettimo Channel. These findings provide a better understanding of the morpho-sedimentary evolution of the Egadi Islands offshore in the latest Quaternary. Moreover, they offer essential scientific support for effectively managing the most valuable priority habitats for conservation, such as the Posidonia oceanica meadow and coralline algae bioconstructions (Coralligenous habitat).