Manganese geochemistry in deep-sea sediments is known to vary greatly over the first few centimeters, which overlaps the in-sediment depth habitats of several benthic foraminiferal species. Here we investigated manganese incorporation in benthic foraminiferal shell carbonate across a six-station depth transect in the Gulf of Lions, NW Mediterranean, to unravel the impacts of foraminiferal ecology and Mn pore water geochemistry. Over this transect water depth increases from 350 to 1987m, while temperature ( ∼ 13°C) and salinity ( ∼ 38.5) remained relatively constant. Manganese concentrations in the tests of living (rose bengal stained) benthic foraminiferal specimens of Hoeglundina elegans, Melonis barleeanus, Uvigerina mediterranea, and Uvigerina peregrina were measured using laser ablation inductively coupled mass spectrometry (laser ablation ICP-MS). Pore water manganese concentrations show a decrease from shallow to deeper waters, which corresponds to a generally decreasing organic-matter flux with water depth. Differences in organic-matter loading at the sediment–water interface affects oxygen penetration depth into the sediment and hence Mn pore water profiles. Mn∕Ca values for the investigated foraminiferal species reflect pore water geochemistry and species-specific microhabitat in the sediment. The observed degree of variability within a single species is in line with known ranges in depth habitat and gradients in redox conditions. Both the Mn∕Ca ratio and interspecific variability hence reflect past Mn cycling and related early diagenetic processes within the sediment, making this a potential tool for bottom-water oxygenation and organic-matter fluxes. Dynamics of both in-sediment foraminiferal depth habitats and Mn cycling, however, limit the application of such a proxy to settings with relatively stable environmental conditions.