The research programs of the BonaRes Module A projects cover a wide spectrum of different processes and related models relevant for soil fertility and other soil functions. To further organize efficient cooperation between the modelers of the different Module A projects and the BonaRes Centre, the third workshop “From Soil Processes to Soil Functions” was organized on the 10th of May 2017 in Halle. The focus of this workshop was on two types of highly relevant processes considered in the modeling approaches of the Module A projects: the carbon and nutrient dynamics in soil, and the soil structure dynamics in response to tillage and biological activity. Both aspects are relevant for the entire set of soil functions evaluated by the systemic modeling approach developed by the BonaRes Centre. We began with a short overview on the state of the art of process understanding at the systemic level of the soil-plant-biome complex. In particular, models on nitrogen, phosphorus, soil organic matter, and soil structure dynamics were presented. During the following round table discussions, existing model concepts and deficiencies were examined. We discussed a mode of cooperation between the Module A projects and the BonaRes Centre, in the framework of understanding and modeling of soil processes relevant for soil functions.