The analysis of d13C in speleothem calcite is established as a palaeoenvironmental proxy, but records can often be complex to interpret due to multiple controls on the signal. Here we present a novel palaeoenvironmental application of non-purgeable organic carbon (NPOC) d13C analysis and compound-specific isotope analysis (CSIA) to speleothems, and compare the resultant signals to a conventional calcite d13C record. By accessing the carbon pool held in molecular organic matter, we are able for the first time to produce stable isotope records complementary to the CO2-derived signal from the speleothem calcite, and begin to identify separate ecological and climatic controls. In this sample from north-west Scotland, the calcite d13C record and the NPOC d13C both show fluctuations at a period of increasing wetness and change from birch woodland to more open peatland, the NPOC signal having a strong correlation with biomarkers for vegetation change. We interpret an inverse correlation between the NPOC and CO2 d13C signals as primarily driven by changes in soil conditions impacting upon microbial activity, with decreased activity leading to a reduction in 13C enrichment of the residual organic matter (the NPOC fraction), and an increase in d13C in the CO2 pool (calcite) due to a decrease in respired 12C. This opens the way for the application of parallel analyses to distinguish between soil conditions and vegetation parameters as the primary control on a record, and highlights the advantage of combining both inorganic and organic geochemical techniques in the palaeoenvironmental interpretation of stable carbon isotopic records.