The research presents the results of a study of the biological productivity and nutrient cycling in two provinces of Kyrgyzstan that differ in their soil and climatic conditions, which consequently affect the biological productivity and nutrient turnover within the soil–plant system. Eastern Issyk-Kul (subboreal belt) is characterized by sufficient moisture and warmth, which favor robust root development and humus formation processes. In mountainous “paratypes” of soils, the total plant biomass accumulates more than in mountain-valley soils. The underground root fraction is dominated by live roots and humified residues, while annual litterfall increases with elevation. In the subtropical belt, in the Kok-Art River basin of the Jalal-Abad region, due to specific climatic conditions, biological productivity, especially the accumulation of underground biomass, is significantly greater than in the subboreal belt. Mountain soils are more susceptible to erosion processes because they are located on slopes of varying steepness and are influenced by numerous factors. One of the main factors protecting the soil from erosion is vegetation cover and the accumulation of root mass in the humus-accumulative horizon. Studies of the biological and ecological properties of soils have shown that soils in the Kok-Art River basin have varying potential fertility, determined by reserves of humus, nitrogen, and other elements.