Following the Deepwater Horizon oil spill (DWHOS), the formation of an unexpected and extended sedimentation event of oil-associated marine snow (MOSSFA: Marine Oil Snow Sedimentation and Flocculent Accumulation) demonstrated the importance of biology on the fate of contaminants in the oceans. We used a wide range of compound-specific data (aliphatics, hopanes, steranes, triaromatic steroids, polycyclic aromatics) to chemically characterize the MOSSFA event containing abundant and multiple hydrocarbon sources (e.g., oil residues and phytoplankton). Sediment samples were collected in 2010–2011 (ERMA-NRDA programs: Environmental Response Management Application – Natural Resource Damage Assessment) and 2018 (REDIRECT project: Resuspension, Redistribution and Deposition of Deepwater Horizon recalcitrant hydrocarbons to offshore depocenter) in the northern Gulf of Mexico to assess the role of biogenic and chemical processes on the fate of oil residues in sediments. The chemical data revealed the deposition of the different hydrocarbon mixtures observed in the water column during the DWHOS (e.g., oil slicks, submerged-plumes), defining the chemical signature of MOSSFA relative to where it originated in the water column and its fate in deep-sea sediments. MOSSFA from surface waters covered 90% of the deep-sea area studied and deposited 32% of the total oil residues observed in deep-sea areas after the DWHOS while MOSSFA originated at depth from the submerged plumes covered only 9% of the deep-sea area studied and was responsible for 15% of the total deposition of oil residues. In contrast, MOSSFA originated at depth from the water column covered only 1% of the deep-sea area studied (mostly in close proximity of the DWH wellhead) but was responsible for 53% of the total deposition of oil residues observed after the spill in this area. This study describes, for the first time, a multi-chemical method for the identification of biogenic and oil-derived inputs to deep-sea sediments, critical for improving our understanding of carbon inputs and storage at depth in open ocean systems.