The data set reports organic carbon (TOC), total carbon (TC), total nitrogen (TN), and total sulfur (TS) concentrations in the upper horizons of deep-sea sediments. The data can further be used to calculate derived parameters total inorganic carbon (TIC=TC-TOC), CaCO3 (TIC*8.3333), and the C/N ratio (TOC/TN). Samples were taken with a Multiple Corer (MUC) and with Push Cores (PUC) that were recovered by the Remotely Operated Vehicle (ROV) KIEL6000 of GEOMAR in Kiel, Germany during two subsequent expeditions with the German Research Vessel SONNE (SO268/1 and SO268/2). Samples originate from six different locations in polymetallic nodule ecosystems in the deep Eastern North Pacific Ocean. Four are situated in the exploration license area of the German Bundesanstalt für Geowissenschaften und Rohstoffe (Federal Institute for Geosciences and Natural Resources; abbreviated BGR) granted by the International Seabed Authority (ISA). These include the Reference Site (GER Reference Site), a site that is designated for a nodule collector prototype trial (GER Trial Site), a site near the Reference Site where a benthic impact experiment (BIE) was carried out (GER Dredge Site) and a site where no polymetallic nodules are found (GER No-Nodule Site). The other two sites were located in the exploration license area of the Belgian company Global Sea Mineral Resources NV (abbreviated GSR): again a Reference Site (BEL Reference Site) and a trial site (BEL Trial Site). The primary aim of the study was to address natural spatial variability in benthic biogeochemistry and characterize baseline conditions in preparation of trials of GSR's pre-prototype polymetallic nodule collector Patania II and for the smaller BIE carried out with a dredge during SO268/2 on 11. to Apr. 2019. Further the dredge area was sampled after the BIE to assess the impacts. Carbon, Nitrogen and Sulfur are determined based on the principle described by Kirsten (1979). Total carbon (TC), total nitrogen (TN), total Sulfur (TS), and total organic carbon (TOC) are analyzed with a Euro EA 3000 Elemental Analyzer (EuroVector Srl, Italy). Samples are collected on board from homogenized wet sediment slices of cores and frozen at -20°C until analysis in the shore lab. In case of PUCs, layers from 2 cores are pooled before homogenizing. In the shore lab, samples are freeze-dried and homogenized by planetary mill (Pulverisette 7, Fritsch, Germany), mortar, and pestle. Two Aliquots are taken from each sample, pre-weighed, and analyzed in two runs. In the first run measurements are conducted both before (for TC, TN, and TS) and after (for TOC) acidification with HCl. In the second run, no acidification is performed and analyses are restricted to C and N. Sulfanilamide standards are used for calibration.