This file contains the biomarker data from the paper Ménot et al., 2025 Organic Geochemistry (https://doi.org/10.1016/j.orggeochem.2025.104982). African low-latitude regions tend to be underrepresented in global continental temperature reconstructions, limiting both our understanding and the reliability of predictions of past and future changes in temperature and precipitation in those parts of the world. The lack of continuous sedimentary archives and quantitative temperature proxies further complicates this issue, especially outside Eastern Africa. Here, we use data collected in Cameroon lakes to assess branched glycerol dialkyl glycerol tetraether (brGDGT)-based temperature proxies and examine potential confounding variables impacting temperature reconstructions. By analyzing GDGT distributions in soil watershed, water column, and surface sediment samples from a total of 11 Cameroon lakes, we could verify that the degree of methylation of brGDGTs (through the MBT′5Me) can serve as a reliable indicator for reconstructing mean annual air temperatures. Additionally, we could confirm that surface water conductivity represents a controlling factor for the brGDGT assemblage in surface sediments of crater lakes. Moreover, we provide the first reconstruction of Mid- to Late-Holocene GDGT-based air temperatures for a crater lake in Cameroon (Central Africa), revealing a temperature decrease of 2.5 °C over the last 7000 years, which agrees with recently published records for East Africa but exceeds current model predictions. These discrepancies highlight the need for additional studies to focus on this geographically underrepresented area.