Multi-proxy temperature reconstructions can provide robust insights into past environmental conditions. By combining different proxies we can disentangle the temperature signal from the indirect climate effects on the environment. This study uses a multi-proxy approach to reconstruct temperature and palaeoenvironmental conditions during the Late Glacial and Early Holocene (13.5–8 cal. ka BP) in the Bohemian Forest, Central Europe. We assessed the similarity of the temperature signal based on chironomids, isoprenoid glycerol dialkyl glycerol tetraether lipids (isoGDGTs), and pollen within a comparison with locally modeled temperature data generated by the CHELSA_Trace21k dataset. Pollen, macroscopic charcoal remains, and geochemistry were further used to reconstruct past environmental conditions such as vegetation dynamics, fire activity, the input of lithogenic material (Titanium), nutrient content (Total Nitrogen) and the sources of organic matter (C/N and δ13Corg). All temperature reconstructions based on independent proxies were positively correlated and followed the same long-term trend. However, results also showed that chironomids-inferred July temperature had lower amplitude variations compared to the other temperature curves. IsoGDGTs showed the most pronounced decrease in temperature values at the onset of the Younger Dryas (YD), corroborating that this cooling event was more marked during winter than summer. However, a decrease of less than 1 °C during summer and two short-term warm events at 12.6 and 12.2 cal ka BP provoked a modest and asynchronous response of the vegetation to the onset of the YD. Nevertheless, isoGDGTs appeared to react to changes in both temperature and organic carbon sources, particularly between 11.2 and 10.6 cal yr BP. These environmental changes, characterized by high values of the GDGT-0/crenarchaeol ratio, recorded an increase in methanogenic activity in the lake sediments, which likely altered the recorded climatic signal. The corresponding anoxic episodes in the lake sediments might be caused by an increasing input of organic carbon from the catchment, related to the development of the vegetation and catchment soils at the beginning of the Holocene. Finally, pollen-based temperature reconstruction showed a lag in the response to major climatic events, such as the onset of YD and Holocene. Our study increases the understanding of the climate-vegetation-environmental feedback during the Late Glacial and Early Holocene in the Bohemian Forest, Central Europe.