The results of our studies on organo-mineral soil clay fractions isolated from long-term fertilization experiments in eastern Germany were compiled. In mineralogical studies it was found that illites were the dominant three-layer minerals in all soil profiles, with the exception of a Dystric Cambisol on gneiss where secondary chlorite is the dominant three-layer mineral. Mineral transformations were observed in unfertilized soils that were observed over a long period and in a soil formation experiment with loamy marl. The investigation of clay-associated organic substances has shown that the organic carbon and total nitrogen concentrations (0.5–10.2% and 0.1–1.2%, respectively) were related to the genetic soil types, to management practices, and to the duration of soil formation processes. This was also true for the quality of organic matter, which was studied by differential thermal analysis (DTA), thermogravimetry (TG) and pyrolysis-field ionization mass spectrometry (Py-FIMS). The latter method enabled the observation of clay-associated organic substances on the basis of molecular subunits. The cation exchange capacities of the clay fractions were closely correlated to the organic carbon concentrations, and therefore dependent on the management practice. Significant correlations were found between the organic matter contents of the clay fractions and physical soil properties such as bulk density and specific gravity, water retention and compressibility. It was concluded that the investigation of the organo-mineral character of soil clay fractions allows a deeper insight into the relationships between organic and inorganic constituents and the properties of soils.