This dataset contains meiofauna abundance data collected from multicore samples (MUC) in several license areas of the Clarion Clipperton fracture Zone (northeast Pacific), an area currently being explored in the light of future polymetallic nodule mining. Seafloor samples were collected onboard RV Sonne during expedition SO239 in 2015. Meiofauna taxa have been counted and identified at different license areas (IOM, GSR, IFREMER) and one Area of Particular Environmental Interest (APEI#3). Each multicore has been analysed in bulk (0-5 cm), except for those of IOM control sites (5 sediment slices, per cm). Meiofauna abundances have been standardized to individuals per 10cm² and are given per taxonomic group (phylum level) and sediment slice (where applicable). Data has been collected and analysed by the Marine Biology Research Group of Ghent University, Belgium.