Abstract The SoilGen1 model was developed to simulate soil development in calcareous loess at Holocene (15,000 BP–present) temporal extent. We used the LEACHC model as a core and added process formulations to describe the effect of vegetation and soil macrofauna on various soil properties. A limited calibration was done on the calcite solubility constant by comparing decarbonization rates in various leaching climates with values predicted by the metamodel of Egli and Fitze [Egli, M. and Fitze, P. 2001. Quantitative aspects of carbonate leaching of soils with differing ages and climates. Catena 46:35–62.]. Soil profiles of C and pH after 15,000 years compared well with measurements in a Belgian loess profile that was never under agriculture, taking the composition of the C-horizon as uniform parent material. Scenarios with and without agriculture, with varying degrees of bioturbation and for documented Holocene climatic and vegetation evolutions in Belgium and Hungary were simulated and compared. Results show a clear effect of bioturbation on soil development, especially in the continental climate evolution of Hungary. Indicators for the possible occurrence of clay migration and disturbance of lateglacial morphology were calculated and these also show the importance of bioturbation.