Geochemical shifts in carbon cycling induced by agriculture in arid and semiarid ecosystems are closely linked to global climate. Here, we evaluated (i) how different agricultural practices in arid steppe ecosystems of north Kazakhstan influenced CO2/O2 exchange rate, respiratory quotient (RQ), and C-transformation efficiency and (ii) shifts in δ13C-CO2 signature induced by long-term and uniform agricultural practices when a natural C3-plant community was substituted with a C3-crop. Conservation tillage and intensive mold-board ploughing were compared with soil that had never been tilled. The content of microbial C was significantly lower in soil subjected to tillage. For all tilled treatments RQ was close to 1.0 and higher than in never tilled soil suggesting complete oxidation of soil organic matter. δ13C-CO2 value for never tilled soil was significantly lower (−26) than in all tilled treatments (around −20), suggesting that agricultural soils produce CO2 with heavier isotope composition compared with undisturbed soil.