•First study on land use–climate interactions in Siberian steppe soils.•Global warming will decrease soil organic carbon stocks in the Siberian steppe.•Losses of soil organic matter due to land-use change are independent from climate.•Mineral-organic associations are susceptible to land-use change.•Climate affects soil microbial communities more than land-use change. The Kulunda steppe is part of the greatest conversion areas of the world where 420,000km2 grassland have been converted into cropland between 1954 and 1963. However, little is known about the recent and future impacts of land-use change (LUC) on soil organic carbon (OC) dynamics in Siberian steppe soils under various climatic conditions. By investigating grassland vs. cropland soils along a climatic gradient from forest to typical to dry steppe types of the Kulunda steppe, our study aimed to (i) quantify the change of OC stocks (0–60cm) after LUC from grassland to cropland as function of climate, (ii) elucidate the concurrent effects on aggregate stability and different functional soil organic matter (OM) fractions (particulate vs. mineral-bound OM), and (iii) assess climate- and LUC-induced changes in the microbial community composition and the contribution of fungi to aggregate stability based on phospholipid fatty acid (PLFA) profiles. Soil OC stocks decreased from the forest steppe (grassland: 218±17Mgha−1) over the typical steppe (153±10Mgha−1) to the dry steppe (134±11Mgha−1). Across all climatic regimes, LUC caused similar OC losses of 31% (95% confidence interval: 17–43%) in 0–25cm depth and a concurrent decline in aggregate stability, which was not related to the amount of fungal PLFA. Density fractionation revealed that the largest part of soil OM (>90% of total OC) was associated with minerals and <10% of C existed in particulate OM. While LUC induced smaller relative losses of mineral-associated OC than particulate OC, the absolute decline in total OC stocks was largely due to losses of OM bound to minerals. This result together with the high 14C ages of mineral-bound OM in croplands (500–2900 yrs B.P.) suggests that mineral-bound OM comprises, in addition to stable OC, also management-susceptible labile OC. The steppe type had a larger impact on microbial communities than LUC, with a larger relative abundance of gram-positive bacteria and less fungi under dry conditions. Our results imply that future drier climate conditions in the Siberian steppes will (i) result in smaller OC stocks on a biome scale but (ii) not alter the effect of LUC on soil OC, and (iii) change the microbial community composition more than the conversion from grassland to cropland.