Soils of mountain ecosystems are one of the most vulnerable ecosystems to climate change, while the ecosystem services they produce are significant and currently at risk. High altitude soils contain high C stocks, but due to difficult access to sites these areas are understudied. Moreover, how the C and N cycling is changing in response to climate change in these ecosystems, is still unclear. Microbial carbon use efficiency (CUE) and its dependency on the environmental constraints along the altitudinal gradients is one important unknown factor. Here we present results from an altitudinal gradient study (3500 to 4500 m a.s.l.) from a Polylepis forest in the Peruvian Andes. We measured the soil organic carbon (SOC) stocks and microbial metabolic CUE by 13C glucose tracing and microbial resource use efficiency (CUEC:N) based on enzyme activity measurements. We expected to find an increase in SOC stock, microbial nutrient limitations, and lower CUE with elevation. SOC stocks depended on soil development and followed a unimodal curve that peaks at 4000 m in two of the three studied valleys. Neither 13CUE nor CUEC:N changed significantly with altitude. Soil C:N ratio, β-glucosidase, chitinase, and phosphatase enzyme activities increased with elevation, but peroxidase activity decreased with elevation. We suggest that more labile organic matter left at high elevation could compensate for the increasing nutrient limitation at high elevation, resulting in no noticeable change in CUE with elevation.