Lignin oxidation products (LOPs) are widely used as vegetation proxies in climate archives, such as sediment and peat cores. The total LOP concentration, Σ8, provides information on the abundance of vegetation, while the ratios C/V and S/V of the different LOP groups also provide information on the type of vegetation. Recently, LOP analysis has been successfully applied to speleothem archives. However, there are many open questions concerning the transport and microbial degradation of LOPs on their way from the soil into the cave system. These processes could potentially alter the original source-dependent LOP signals, in particular the C/V and S/V ratios, and thus complicate their interpretation in terms of past vegetation changes. We analyzed LOPs in leaf litter and different soil horizons as well as dripwater and flowstone samples from four different cave sites from different vegetation zones in New Zealand using ultrahigh-performance liquid chromatography coupled to high-resolution mass spectrometry. We test whether the original source-dependent LOP signal of the overlying vegetation is preserved and can be recovered from flowstone samples and investigate how the signal is altered by the transport from the soil to the cave. The LOP concentrations range from mg g−1 in the soil to ng g−1 in the flowstones. Our results demonstrate that, from the soil to the flowstone, the C/V and S/V ratios both increase, while the total lignin content, Σ8, strongly decreases. This shows that the LOP signal is strongly influenced by both transport and degradation processes. Nevertheless, the relative LOP signal from the overlying soil at the different cave sites is preserved in the flowstone. We emphasize that for the interpretation of C/V and S/V ratios in terms of past vegetation changes, it is important to compare only samples of the same type (e.g., speleothem, dripwater or soil) and to evaluate only relative variations.