The contribution of soil organic matter (SOM) to continental margins is largely ignored in studies on the carbon budget of marine sediments. Detailed geochemical investigations of late Quaternary sediments (245–0 ka) from the Niger and Congo deep-sea fans, however, reveal that Corg/Ntot ratios and isotopic signatures of bulk organic matter (δ13Corg) in both fans are essentially determined by the supply of various types of SOM from the river catchments thus providing a fundamentally different interpretation of established proxies in marine sciences. On the Niger fan, increased Corg/Ntot and δ13Corg (up to −17‰) were driven by generally nitrogen-poor but 13C-enriched terrigenous plant debris and SOM from C4/C3 vegetation/Entisol domains (grass- and tree-savannah on young, sandy soils) supplied during arid climate conditions. Opposite, humid climates supported drainage of C3/C4 vegetation/Alfisol/Ultisol domains (forest and tree-savannah on older/developed, clay-bearing soils) that resulted in lower Corg/Ntot and δ13Corg (< −20‰) in the Niger fan record. Sediments from the Congo fan contain a thermally stable organic fraction that is absent on the Niger fan. This distinct organic fraction relates to strongly degraded SOM of old and highly developed, kaolinite-rich ferallitic soils (Oxisols) that cover large areas of the Congo River basin. Reduced supply of this nitrogen-rich and 12C-depleted SOM during arid climates is compensated by an elevated input of marine OM from the high-productive Congo up-welling area. This climate-driven interplay of marine productivity and fluvial SOM supply explains the significantly smaller variability and generally lower values of Corg/Ntot and δ13Corg for the Congo fan records. This study emphasizes that ignoring the presence of SOM results in a severe underestimation of the terrigenous organic fraction leading to erroneous paleoenvironmental interpretations at least for continental margin records. Furthermore, burial of SOM in marine sediments needs more systematic investigation combining marine and continental sciences to assess its global relevance for long-term sequestration of atmospheric CO2.