Abstract Lipid extracts from four long-term experiments (Broadbalk Wilderness, Geescroft Wilderness, Hoosfield Spring Barley and Park Grass) were analysed using a combination of gas chromatography, gas chromatography–mass spectrometry and gas chromatography–combustion–isotope ratio mass spectrometry. The lipid content of the primary organic inputs for each soil were also analysed in order to assess the early diagenetic fate of the various compound classes present. Soil pH was observed to, either directly or indirectly, have a significant effect on lipids with a relative increase in abundance of n-alkanes at higher pH (7.31) and a large relative increase in n-alkanoic and ω-hydroxy acids at low pH (3.74). Triacylglycerols exhibited severe losses irrespective of pH. In an arable soil, n-alkanoic acids showed a temporal decrease in concentration whilst levels of n-alkanols remained static, the difference was ascribed to a more rapid turnover and possible leachate migration of the n-alkanoic acids. The phytosterol, sitosterol, was observed to rapidly diminish in soils possibly as a result of assimilation by soil dwelling invertebrates. Analysis of 5β-stigmastanol (a faecal biomarker) showed that it remained at levels indicative of manuring even after 113 years. Furthermore, analysis of 5β-stanyl esters revealed a manuring signal even more persistent than that exhibited by the free stanols. Knowledge of the biogeochemical cycling of lipids in the soil environment will help facilitate understanding of the processes which underpin carbon cycling in soils.