These data are from the paper entitled Biotic induction and microbial ecological dynamics of Oceanic Anoxic Event 2, published in Communications Earth & Environment (Connock et al., 2022). In this work 43 powdered core samples were collected over a ~10m sediment core covering ocean anoxic event 2 (OAE-2) and spanning the Cenomanian-Turonian boundary (~93.9 Ma) at ODP Site 207-1258 on the Demerara Rise. Application of a new LC-qTOF-MS method revealed a diverse molecular fossil record comprising cyclic tetrapyrroles (including free base chlorins, porphyrins, and metalloporphyrins), isorenieratane, dialkyl glycerol ethers (DAGEs), extended archaeols, butanetriol/pentanetriol dialkyl glycerol tetraethers (BDGT/PDGT), and glycerol dialkyl glycerol tetraethers (GDGTs), including isoprenoidal GDGTs (isoGDGTs, such as crenarchaeol), branched GDGTs (brGDGTs) and overly-branched GDGTs (obGDGTs). The distributions of these biomarkers reflect microbial communities residing at specific water depths ranging from epipelagic to benthic settings, which enabled the reconstruction of microbial ecological and paleoceanographic dynamics in the southern proto-North Atlantic Ocean before, during, and after OAE-2.