An experimental approach was developed to assess the individual and combined effects of two climate change stressors (seawater temperature and POC quality) on deep-sea benthic macrofaunal assemblages. Sediment samples were collected from the bathyal continental slope of the Cabo Verde Basin (CVB, Equatorial Atlantic) in August 2021. The data originate from a controlled onboard experiment using stable isotope tracers (13C and 15N) to simulate climate change projections. A total of 19 sediment cores, obtained via four multi-corer deployments, were subjected to four treatments: a control, increased temperature (+2 °C), reduced POC quality (dialysed labile fraction), or a combination of both. Following a 48-hour incubation period, the macrofaunal organisms were fixed, sieved (300 µm mesh), sorted, and identified. The resulting dataset includes quantitative measurements of macrofaunal abundance, biomass, and taxonomic composition.