Near-bottom multibeam bathymetry and back-scatter data acquired along the Amorgos and Santorini-Amorgos faults, in the Aegean sea. High-resolution bathymetry data (1 m/pixel) were acquired by the autonomous underwater vehicle (AUV) IdefX, deployed during the AMORGOS-22 cruise (https://doi.org/10.17600/18001479) with the MBES EM2040. The dataset consists of six DEMs as well as fourteen back-scatter mosaics (i.e. two versions for each dives, raw and processed (compention of the antenna diagram)). In addition, a DEM extracted from dive 2 is provided. The bathymetric data were processed with GLOBE, while the back-scatter data were processed with Sonarscope. Renavigation of the vehicule was necessary during processing and is applied to both the bathymetric grids and backscatter mosaics. Files are provided in TIF format, projected in UTM 35 N (WGS 84).