The presented data set represents a comprehensive characterization of soil samples that were used in the German joint research priority program 2322 ”SoilSystems: Systems ecology of soils – energy discharge modulated by microbiome and boundary conditions” funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). The joint research program SoilSystems aims to integrate a thermodynamic description of the soil system for the first time in order to gain a systemic view on energy and matter fluxes and their interactions with living and non-living soil components. These include numerous aspects and parameters of soil (organic matter) chemistry, soil microbiology (including faunal trophic levels) and the new discipline of soil thermodynamics. In order to have a joint focus in the individual research activities, a ‘Common Experimental Platform’ has been set up. The provision of shared soil samples, substrates and incubation conditions should enable coherent and interlinked data to be obtained. More information can be found here: https://soilsystems.net/.