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. Samples were dried at 45°C and calcareous organisms acidified before a second drying. Individual organisms from different sediment layers of the same core were pooled (polychaetes into feeding guilds) to obtain enough biomass for isotope measurements. Dried samples were analyzed for dry mass, carbon and nitrogen content, and stable isotope signatures (δ13C, δ15N).