AbstractClimate and parent material strongly control vegetation structure and function, yet their control over the belowground microbial community is poorly understood. We assessed variation in microbial lipid profiles in undisturbed forest soils (organic and surface mineral horizons) along an altitudinal gradient (700, 1,700, and 2,700 m a.s.l. mean annual temperature of 12–24°C) on two contrasting parent materials (acidic metasedimentary vs. ultrabasic igneous rock) in Mt. Kinabalu, Borneo. Soil organic carbon and nitrogen concentrations were generally higher at higher altitudes and, within a site, at upper soil horizons. Soil pH ranged from 3.9 to 5.3, with higher values for the ultrabasic soils especially at higher altitudes. The major shifts in microbial community structure observed were the decline in the ratio of fungal to bacterial lipid markers both with increasing soil depth and decreasing altitude. The positive correlation between this ratio with soil C and N concentrations suggested a strong substrate control in accord with the literature from mid to high‐latitude ecosystems. Principal component analysis using seven groups of signature lipids suggested a significant altitude by parent material interaction—the significant difference in microbial community structure between the two rock types found at 2,700‐m sites developed on weakly weathered soils diminished with decreasing altitude towards 700‐m sites where soils were strongly weathered. These results are consistent with the hypothesis that parent material effect on soil microbial community (either directly via soil geochemistry or indirectly via floristic composition) is stronger at an earlier stage of ecosystem development.