Lipid biomarkers [fatty acids (FAs), sterols and alcohols] and total organic carbon (TOC) were analyzed in 48 surface (0–2 cm) sediment samples collected twice (winter 2008/2009 and summer/2009) in two transects ranging from 25 to 3,000 m depths. This sampling array encompassed the major upwelling region in the southeastern Brazilian continental margin, where the river influence is probably minimal. The objectives were (1) to evaluate the sources, transport and major areas of organic matter (OM) accumulation in the continental margin and (2) to identify the fraction of OM that is potentially available to secondary benthic producers. As expected from the regional oceanographic characteristics, lipids derived from primary and secondary autochthonous producers (0.073–5.3 mg gTOC−1) made the major fraction of the sedimentary OM, whereas lipids from allochthonous sources (0.043–0.40 mg gTOC−1) and from bacteria (<0.01–0.43 mg gTOC−1) were of relatively less importance. The accumulation of OM in the sediments was highly dependent on the coupling of physical (hydrodynamics) and biological (response to upwelling) factors. It was found that while some restricted areas in the shelf was a sink of labile OM, the export of this material to the upper and middle slope (400–1,000 m depths) can represent an important source of bioavailable OM to the deep sea benthic community.