The paper presents the results of studies aimed at assessing the variability of respiratory activity of soil microbiota (rates of basal and substrate-induced respiration), as well as of the content of organic matter carbon and microbial biomass carbon in soils formed and functioning in natural (slightly damaged) biogeocenoses along altitudinal gradient from the foothills to the high mountain regions of the Central Caucasus (500-3500 m a.s.l., Elbrus variant of altitudinal zonality, Kabardino-Balkaria). It is shown that the mean values of the studied indicators in surface horizons (0-10 and 0-20 cm, depending on the soil type) significantly increase with the altitude from mountain chernozems to subalpine mountain-meadow soils and significantly decrease at the maximum altitude in the zone of alpine mountain-meadow soils. The studied indicators in different soil types within the same altitudinal zone also differ; this difference is statistically significant (t > 2.5; p < 0.02) for most of the indicators for the compared pairs of soil types. The data obtained indicate that the impact of the altitudinal gradient is significantly transformed by additional factors. The multi-regression analysis has been performed to identify the effect of the main factors of relief (elevation above sea level and slope aspect and steepness) and climate (19 bioclimatic characteristics) on the studied indicators. It shows that the mean cumulative contribution of all 22 factors to the variation of the studied indicators is 40% in mountain chernozems, 66% in mountain-meadow chernozem-like soils, 31% in mountain meadow-steppe subalpine soils, 67% in subalpine mountain-meadow soils, and 67% in alpine mountain-meadow soils. Thus, the effect of the considered factors may significantly differ both for soils located along the altitudinal gradient and for soils functioning within the same altitudinal zone. Relief and climate play an important, but not the only, role in the formation of properties of mountainous soils in the Central Caucasus.