Fossil organic matter (OM) in Paleoarchean rocks is an invaluable tracer of ancient life, yet it is often contentious due to low preservation potentials of its original organic molecular characteristics under generally high metamorphic grades. This study reports on exceptionally preserved OM within black smoker-type sulfide mineralizations from the 3.24 billion-years-old Sulphur Springs volcanic-hosted massive sulfide deposit, East Pilbara Terrane, northwestern Australia. Fine scale mineralogical and organic molecular variations – documented by SEM and TEM techniques, Raman and FTIR Spectroscopy, as well as ToF-SIMS analysis – trace the formation of millimetre-scale pyritic hydrothermal orifices. Overmature OM (≳200–250 °C) enriched in aromatic hydrocarbons occurs within earliest formed colloform-banded pyrite that could have precipitated at high temperature upon mixing of hot hydrothermal fluids with cold seawater. In contrast, mature OM (within the catagenesis window; ∼100–150 °C) with lower proportions of aromatic hydrocarbons occasionally occurs alongside pyrite within barite near the inner paleofluid conduits of the hydrothermal orifices. A deposition of this OM generation from cooler fluids enriched in sulfate during waning hydrothermal activity is corroborated by its association with original mineralogy, particularly the occurrence of isolated nanoinclusions of OM within hydrothermal barite away from grain boundaries or fissures and cracks, which renders impossible an origin from post-depositional hydrocarbon migration. When compared to the overmature OM within colloform-banded pyrite, the better-preserved inner OM not only contains less abundant, smaller, and less ordered aromatic hydrocarbons, but also higher amounts of aliphatic molecules with longer chain lengths and higher proportions of carbonyl and amide functional groups. Although the latter characteristics are consistent with contributions by microbial biomass, abiotic origins are equally plausible because hydrothermal processes can produce OM with similar organic molecular attributes. Irrespective of these uncertainties on the ultimate sourcing of OM, common intergrowths of the cooler OM with nanoscopic iron oxides – hematite and lesser magnetite – hint at its hydrothermal deposition from colloidal particles that have been stabilized by iron-organic complexation. Further research is required to ascertain the significance of this process for the hydrothermal cycling and release of organic carbons and bound iron into the Paleoarchean oceans. Collectively, our results show that ancient marine hydrothermal systems can preserve OM with differing degrees of thermal degradation, which allows for insights into its sourcing, cycling, and deposition.