The dataset contains colour parameters and sedimentological and paleogenomic data for two Calypso cores (giant piston cores), recovered at the same station on the Eirik Drift (Labrador Sea, North Atlantic) during the ice2ice cruise GS16-204 with RV G.O. Sars. The sediments investigated cover the last ca. 50,000 years with higher resolution around Heinrich Event 4 and Glacial Interstadial 8, as well as during the deglaciation. We measured colour parameters in GS16-204-22CC-A and GS16-204-22CC-B to stratigraphically tie both cores together. We measured stable isotope data from GS16-204-22CC-A, and ice rafted debris data and radiocarbon ages from GS16-204-22CC-B to transfer the published age model for GS16-204-22CC-A (Griem et al. 2019) to GS16-204-22CC-B where we did our paleogenomics study. The dataset also contains simplified metabarcoding data for the last 50,000 years for GS16-204-22CC-B. The full metabarcoding dataset is available from the European Nucleotide Archive repository via accession number PRJEB112075.