The combined use of plant wax n-alkane δD and branched glycerol dialkyl glycerol tetraether lipids (brGDGT) provide a novel approach for paleoaltitude reconstructions. Previous studies from East Africa, however, revealed inconsistent results between the proxy estimates and altitudinal parameters. Here, we explore these proxies in soils of different land use (forest, cropland and pasture) along an altitudinal transect in the Jimma zone of the southwest Ethiopian highlands to better understand environmental and plant-specific factors controlling the isotopic composition and distribution of n-alkanes and brGDGTs. The hydrogen isotope composition of individual n-alkanes does not unambiguously reflect the altitude effect on precipitation δD, but seems largely influenced by the specific land use. Only forest soil-derived n-C27 and n-C29 alkane δD values exhibit a significant linear relation with altitude (r = -0.87, p < 0.05), likely reflecting the most stable ecosystem. The resulting lapse rate of -17‰/1000 m is comparable with that of local precipitation in the southwest Ethiopian highlands. In addition, the linear correlation of the average chain length (ACL) and δ13C values of forest soil n-alkanes suggests a physiological adaptation of the specific plant type waxes to altitude-induced environmental changes in the study area. The distribution of brGDGTs also reveals a significant linear correlation with altitude (r = -0.97, p < 0.01), reflecting the decrease in temperature with higher elevation independent of land use. In addition, brGDGT-based mean annual air temperature estimates (MAT) of 19.5°C to 14.0°C and temperature lapse rate of -6°C/1000 m are in good agreement with direct measurements in the Jimma zone. In contrast to previous studies from East Africa, our results show that both soil n-alkane δD values and brGDGT-based MAT distributions track present day altitude effects on local environmental gradients in the southwest Ethiopian highlands.