Changes in soil fungal biomass ergosterol, microbial biomass and their role in soil organic carbon (SOC) dynamics along elevation and depth gradients in the Alps are still poorly explored. We investigated changes in stocks of SOC, total N, microbial biomass C (MBC) and N (MBN) and fungal biomass ergosterol at different elevation levels (low, mid and high) in two alpine sites. These two alpine sites represent similar temperature and precipitation regimes, one on alkaline (Hochschwab) the second on acidic (Rauris) bedrock. The stocks of MBC increased with elevation in both sites ranging from 37.6 to 126.1 g m^–2, and MBN stocks from 4.1 to 19.8 g m^–2, following the changes in SOC and total N stocks, except at alkaline low elevation level. The stocks of MBC and MBN were higher at mid-elevation in alkaline than in acidic site. In contrast, MBN stocks were higher at low and high elevation level in acidic site compared to those in alkaline site. Median ergosterol stocks varied around 0.4 g m^–2 in alkaline and increased from 0.05 to 0.2 g m^–2 in acidic site. At all elevation levels, microbial biomass-C/N (MB-C/N) ratio in alkaline site increased with soil depths from 6.0 to 12.3 and remained constant in acidic site between 4.9 and 6.8. In alkaline site, the ratios of ergosterol/MBC declined from 0.6 to 1.4% at 5 cm depth to values around 0.2% at 15–25 cm depth, while this ratio varied between 0.4 and 0.1% at all soil depths in acidic site. In both sites, redundancy and variation partition analysis showed that soil microbial properties were driven by soil chemical properties rather than environmental variables. Our results suggest that environmental variables were less disruptive to soil fungal and microbial biomass and inherent soil properties drive changes in soil microbial and fungal biomass stocks and may drive changes in microbial community structure.