The scientific exploration of Mallorca Channel seamounts (western Mediterranean) is improving the knowledge of the Ses Olives (SO), Ausias March (AM), and Emile Baudot (EB) seamounts for their inclusion in the Natura 2000 network. The aims are to map and characterize benthic species and habitats by means of a geological and biological multidisciplinary approach: high-resolution acoustics, sediment and rock dredges, beam trawl, bottom trawl, and underwater imagery. Among the seamounts, 15 different morphological features were differentiated, highlighting the presence of 4000 pockmarks, which are seafloor rounded depressions indicators of focused fluid flow escapes, usually gas and/or water, from beneath the seabed sediments. So far, a total of 547 species or taxa have been inventoried, with sponges, fishes, mollusks, and crustaceans the most diverse groups including new taxa and new geographical records. Up to 29 categories of benthic habitats have been found, highlighting those included in the Habitats Directive: maërl beds on the summits of AM and EB, pockmarks around the seamounts and coral reefs in their rocky escarpments as well as fields of Isidella elongata on sedimentary bathyal bottoms. Trawling is the main demersal fishery developed around SO and AM, which are targeted to deep water crustaceans: Parapenaeus longirostris, Nephrops norvegicus, and Aristeus antennatus. This study provides scientific information for the proposal of the Mallorca Channel seamounts as a Site of Community Importance and for its final declaration as a Special Area of Conservation.