This dataset contains biogeochemical solid-phase and pore water data from sediment core MOZ4-CS03 (named S2-PE in the publication cited below), collected on 14 November 2015 during the PAMELA-MOZ4 oceanographic cruise offshore northwest Madagascar. Core MOZ4-CS03 represents a non-seep reference site and was investigated to provide a baseline for comparison with methane-seep sediments from nearby pockmark site MOZ4-CSF04, enabling assessment of the impact of fluid seepage on sediment biogeochemistry and diagenetic processes. Solid-phase parameters comprise total organic carbon (TOC), stable carbon isotopes of organic matter, reactive iron phases (dithionite-extractable Fe), pyrite content (FeS2) and its sulfur isotopic composition (δ34S), carbonate mineralogy (calcite, high Mg-calcite, aragonite), and stable carbon and oxygen isotopes of background carbonates. Bulk elemental concentrations of Fe and Al were determined by X-ray fluorescence (XRF). Pore water analyses include dissolved methane (CH4), sulfate (SO4), sulfide (H2S), dissolved iron (Fe), manganese (Mn), calcium (Ca), magnesium (Mg), total alkalinity (TA), and stable carbon isotopic compositions of methane and dissolved inorganic carbon (DIC). The dataset also includes porosity measurements.