Carbon and nitrogen are stabilized in soil organic matter (SOM) through physical protection by soil aggregates, chemical protection by associations with soil minerals (clay and silt particles) and biochemical protection by recalcitrance.  The objective of this study was to evaluate total N and organic C stocks across a wide range of European ecosystems, differing in land use, soil type and climate, and how those factors affect the distribution of C and N within physically and chemically defined pools of unprotected and protected SOM.  Soils were sampled to 30 cm depth from 11 sites of the NitroEurope (NEU) level 3 site network (4 cropland, 3 coniferous forest, 1 deciduous forest, and 3 grassland sites) and analyzed for soil organic C (SOC) and total N (TN), and whole soil δ¹³C and δ¹⁵N at different depths.  Surface samples (0-5 cm) were fractionated using two different methods into aggregate-protected versus non-protected C and N pools, particulate organic matter (POM) and mineral-associated C and N, and biochemically recalcitrant and non-recalcitrant mineral-associated C and N pools. This study showed very low TN stocks at deeper depths in the coniferous forest sites; distinct SOC, TN, δ¹³C and δ¹⁵N patterns through the soil profile depending on land-use; much lower C and N associations with silt and clay minerals at cropland versus forest and grassland sites; and revealed total POM as a strong driver for total soil C and N differences among all sampled sites.