In a lysimeter experiment with juvenile beech trees (Fagus sylvatica L.) we studied the development of depth gradients of soil organic matter (SOM) composition and distribution after soil disturbance. The sampling scheme applied to the given soil layers (0-2 cm, 2-5 cm, 5-10 cm and 10-20 cm) was crucial to study the subtle reformation of SOM properties with depth in the artificially filled lysimeters. Due to the combination of physical SOM fractionation with the application of ¹⁵N-labelled beech litter and ¹³C-CPMAS NMR spectroscopy we were able to obtain a detailed view on vertical differentiation of SOM properties. Four years after soil disturbance a significant decrease of the mass of particulate OM (POM) with depth could be found. A clear depth distribution was also shown for carbon (C) and nitrogen (N) within the SOM fractions related to bulk soil. The mineral fractions <63 μm clearly dominated C storage (between 47 to 60% of bulk soil C) and N storage (between 68 to 86% of bulk soil N). A drastic increase in aliphatic C structures concomitant to decreasing O/N-alkyl C was detected with depth, increasing from free POM to occluded POM. Only a slight depth gradient was observed for ¹³C but a clear vertical incorporation of ¹⁵N from the applied labelled beech litter was demonstrated probably resulting from faunal and fungal incorporation. We clearly demonstrated a significant reformation of a SOM depth profile within a very short time of soil evolution. One important finding of this study is that especially in soils with reforming SOM depth gradients after land-use changes selective sampling of whole soil horizons can bias predictions of C and N dynamics as it overlooks a potential development of gradients of SOM properties on smaller scales.