Perennial wheat yields for several years after sowing, and develops a deep and dense root system, thereby improving soil structure and preserving soil fertility. It is also drought resistant, which increases its future potential under the ongoing climate change. Moreover, perennial wheat offers and effective strategy for carbon sequestration through increasing soil carbon stocks. However, the effect of perennial wheat on soil properties remains uncertain in the conditions of south-eastern Kazakhstan due to the lack of data. To fill this gap, we conducted a study in which five varieties of perennial wheat were grown in the Almaty region in soils of different fertility for two years. As a result, in the plot where topsoil was removed to a depth of 25 cm, total carbon increased by nearly three times, from 0.54% to 1.42%, and the number of microorganisms increased from 715.1x103±0.2x103 to 48.0x103±0.6x103 colony forming units per ml of soil. The photosynthetic performance of perennial wheat varieties in the experimental plot was not negatively affected by the removal of top soil suggesting that perennial wheat can successfully restore soil fertility and replenish soil with chemical elements involved in photosynthesis. Our results confirm that in the conditions of the south-eastern Kazakhstan perennial wheat makes a significant contribution to the soil carbon stock accumulation and development of soil biota; in our study, these effects were particularly strong in the case of degraded soil.