We studied the factors which regulate microbial community organization in soils of managed ecosystems. Soil microbial biomass C and N (SMBC, SMBN), EC/ENIN ratio, ergosterol, and phospholipid fatty acids (PLFA) were determined in organically fertilised meadows and grasslands with abandoned management at three sites (Stubai Valley, Passeier Valley, and Monte Bondone) to study the relative importance of the factors site and management in governing the variability of soil microbial biomass and community structure in subalpine grasslands of the European Alps. Our data provide evidence that management abandonment has important effects on the structure of the soil microbial biomass, namely an increase in the fungal biomass. SMBC, SMBN, EC/ENIN ratio and ergosterol contents differed significantly between sites. SMBC was similar in abandoned and managed grasslands, whereas SMBN was lower and ergosterol contents were higher in abandoned grasslands as compared to managed meadows. We concluded that the impact of management abandonment on soil microbial biomass was of relatively less importance than effects of site and sampling time, and the effect of abandonment may be better detected at the community scale of resolution.