We present elemental, lipid biomarker and, in the supplement, compound-specific isotope (δ13C, δ2H) data for soils and leaf litter collected in the catchment of Lake Ohrid (Albania, Macedonia), as well as macrophytes, particulate organic matter and sediments from the lake itself. Lake Ohrid provides an outstanding archive of continental environmental change of at least 1.2 million years and the purpose of our study is to ground truth organic geochemical proxies that we developed in order to study past changes in the terrestrial biome. We show that soils dominate the lipid signal of the lake sediments rather than the vegetation or aquatic biomass. There is a strong imprint of suberin monomers on the composition of total lipid extracts and chain-length distributions of n-alkanoic acids, n-alcohols, ω-hydroxy acids and α, ω-dicarboxylic acids. Our end-member survey identifies that ratios of mid-chain length suberin-derived to long-chain length cuticular-derived alkyl compounds as well as their average chain length distributions can be used as new molecular proxies of organic matter sources to the lake. We tested these for the 8.2 ka event, a pronounced and widespread Holocene climate fluctuation. In SE Europe climate became drier and cooler in response to the event, as is clearly recognisable in the carbonate and organic carbon records of Lake Ohrid sediments. Our new proxies indicate biome modification in response to hydrological changes, identifying two phases of increased soil organic matter (OM) supply, first from soils with moderately degraded OM and then from more degraded soils. Our study demonstrates that geochemical fingerprinting of terrestrial OM should focus on the main lipid sources, rather than the living biomass. Both can exhibit climate-controlled variability, but are generally not identical.