This dataset was collected during the expeditions 'GS2016109A', 'GS2017110', and 'GS2018108' of research vessel G.O.SARS to the Schulz Bank seamount (Arctic Mid-Ocean Ridge) in 2016, 2017 and 2018. It includes amplicon raw sequence reads (V3V4 region 16S rRNA gene survey) of seawater and deep-sea sponge-associated microbes. The sponge species Geodia hentscheli, Lissodendoryx complicata, and Schaudinnia rosea are covered.