Elevated organic matter (OM) concentrations are found in hadal surface sediments relative to the surrounding abyssal seabed. However, the origin of the biological material remains elusive. Here, we report the composition and distribution of cellular membrane intact polar lipids (IPLs) extracted from surface sediments around the deepest points of the Atacama Trench and adjacent bathyal margin to assess and constrain the sources of labile OM in the hadal seabed. Multiscale bootstrap resampling of IPLs’ structural diversity and abundance indicates distinct lipid signatures in the sediments of the Atacama Trench that are more closely related to those found in bathyal sediments than to those previously reported for the upper ocean water column in the region. While the overall number of unique IPL structures in hadal sediments is limited and they contribute a small fraction of the total IPL pool, they include a high contribution of phospholipids with mono- and di-unsaturated fatty acids that are not associated with photoautotrophic sources. The diversity of IPLs in hadal sediments of the Atacama Trench suggests the presence of in situ microbial production and biomass that resembles traits of physiological adaptation to high pressure and low temperature, and/or the transport of labile OM from shallower sediment. We argue that the export of the most labile lipid component of the OM pool from the euphotic zone and the overlying oxygen minimum zone into the hadal sediments is neglectable. Our results contribute to the understanding of the mechanisms that control the delivery of labile OM to this extreme deep-sea ecosystem. Furthermore, they provide insights into some potential physiological adaptation of the in situ microbial community to high pressure and low temperature through lipid remodeling.