Seabed mapping represents a very useful tool for seascape characterization and benthic habitat study, and requires advanced technologies for acquiring, processing and interpreting remote data. Particularly, acoustic instruments, such as high-resolution swath bathymetry sounder (i.e., Multibeam Echosounder: MBES), allows to recognize, identify and map the extension of benthic habitats without applying invasive mechanical procedures. Bathymetry and backscatter (BS) data are crucial to perform modern habitat mapping, however they require careful end-product development and, to date, no standardized procedure exists. In this work, a protocol for benthic habitat mapping, with focus on coralligenous bioconstructions, was developed using the open-source software QGIS. This protocol, tested within the Isola Capo Rizzuto Marine Protected Area (Calabria, Italy), is designed to be freely reproducible by researchers working in the field of marine ecosystem monitoring and conservation. Through the proposed mapping procedure, it is possible to: i) identify benthic habitats on selected study areas by combining bathymetry and BS data with geomorphological indices performed in QGIS; ii) quantitatively define the 2D and 3D distribution of coralligenous bioconstructions in terms of surface covered, thickness and volume. Moreover, the statistical analysis of quantitative morphometric data allowed for comparison of geometric characteristics of different coralligenous morphotypes. The obtained results, combined with improvement of minimally invasive sampling and geobiological–geochemical characterization, can contribute to the development of protocols aimed at monitoring marine bioconstructed ecosystems, many of which protected by national and international regulations due to their importance for Mediterranean biodiversity preservation, and plan actions for their protection and persistence.