The present investigation focuses on the Global Sea Mineral Resources contract area B4S03 site in the Clarion-Clipperton Fracture Zone nodule fields. We investigated the sedimentary characteristics and the higher-taxon (order/class) and lower-taxon (family, morphospecies) diversity of the soft sediment macrobenthos with special focus on the dominant taxa (Isopoda, Polychaeta, Tanaidacea) in relation to nodule abundance. Across all analyses no consistent and/or significant differences between the two nodule-rich and the nodule free stations were found in terms of abiotic or biotic factors, suggesting that both habitat-types have similar sedimentary conditions and that macrofauna is represented by comparable densities and higher-taxon diversity across stations. Rarefaction/accumulation curves and sample coverage analysis shows that the current sampling effort was insufficient to characterize the B4S03 site diversity at morphospecies level but covered >90% of the diversity at the family level for the three dominant taxa. The high number of singletons encountered, the patchiness and low densities of the investigated taxa coupled to the logistically limited potential for replication per habitat/station, may point to under-sampling bias of the current study with the risk to underestimate species diversity and overestimate endemism. We recommend a more extensive sampling with the combination of molecular tools coupled with taxonomical expertise.