A catalytic hydropyrolysis procedure was developed for rapidly assessing the relative abundances and variety of different biomarker lipid structures in microbial cultures by reductively converting free functionalised and polymeric lipids within whole cells into hydrocarbons. High pressure hydrogen gas and a molybdenum catalyst were used to target and cleave carbon-oxygen covalent bonds (particularly ester, alcohol, acid and ether) and the pyrolysis process was conducted in an open-system reactor configuration to minimise structural and stereochemical rearrangements in the products. A revised experimental protocol, involving a modified catalyst-loading procedure, careful use of a silica support substrate and a revised temperature program was tested and optimised for handling biomass. Partial hydrogenation of double bonds inevitably did occur although it was found that some unsaturation was preserved, particularly within branched and polycyclic hydrocarbon structures. This experimental approach aids our ability to optimally correlate fossil biomarker signals found in the sedimentary record with their lipid precursors found in extant organisms. Our technique complements more rigorous, but time-consuming, chemical approaches used for elucidating the exact chemical structures of intact functionalised lipids by providing a rapid means by which to screen microbial cultures.