We processed and analyzed molluscan shells from three cold-water coral sediment cores from the Alboran Sea (western Mediterranean Sea) to investigate palaeoceanographic and habitat characteristic drivers of molluscan diversity in a cold-water coral reef over the last 13,000 years. The three sediment cores are GeoB13728-2, GeoB13729-1, and GeoB13730-1. For each of the cores, we provide here the (a) the age models and aggradation rate calculations; (b) CT data including coral clast size, coral clast orientation, sediment density, and total coral content; and (c) abundance and diversity data for all molluscan species, feeding groups, and mobility groups encountered. We also provide (d) new U/Th coral ages for cores GeoB13728-2 and GeoB13730-1 as well as (e) re-calibrated AMS 14C coral ages for all three sediment cores.