With a projected world population of about nine billion people in 2050 and the increasing threat of global climate change, agriculture will be forced to develop management strategies that will ensure food security and increase the soil's ability to store CO2. The fertility of a soil depends heavily on the activity of soil microorganisms as the main drivers of all nutrient cycles. At the same time, soil microorganisms also contribute to the stabilization of organic carbon (OC) by promoting aggregate formation. In addition, there is increasing evidence that soil organic matter (SOM) is predominantly of microbial origin. While both organic and mineral fertilization are assumed to increase soil organic carbon stocks, it is not yet fully understood how and to what extent these different fertilizers influence the composition and activity of soil microorganisms and hence, the turnover or stabilization of SOM. The present work was intended to answer this question by analyzing soil samples from the Static Fertilization Experiment Bad Lauchstädt. Five different fertilization treatments as well as the non-fertilized control were investigated. Beside the crop-specific fertilization also the presence of symbioses as an additional source of minerals was considered. In this context, the sampling was carried out on two strips, being different in both the crop type at sampling time (alfalfa as host plant for rhizobia and arbuscular mycorrhizal fungi (AMF) vs. sugar beet as non-host plant) as well as in their crop rotation (with legume vs. without legume). As an essential finding both the individual and the combined use of the two fertilizer types were found to promote C stabilization in agricultural soils. However, the results show that the capacity of a soil for C stabilization is limited. Thus, the soil-specific C saturation deficit should be taken into account in the search for a suitable fertilization strategy in addition to the plant-specific nutrient requirement.