In this study, we measured the stocks and pool sizes of soil organic carbon (SOC) and total soil nitrogen (TN), and their natural 13C and 15N abundance across a wide range of temperate European ecosystems. The objectives were to examine any distinct isotope patterns with land use or climate, and how C and N in these different ecosystems are distributed among soil organic matter (SOM) fractions to better predict soil C and N dynamics and longer term persistence. Soils were sampled to 30 cm depth at 11 sites of the Nitro Europe (NEU) network and included four forests, three grasslands and four croplands. Surface soil samples were fractionated using a combined size-density fractionation protocol separating light (LF) from heavy particulate organic matter (hPOM) by density and silt-from-clay-associated SOM by size. Down-profile natural abundance 15N patterns pointed towards a closed N cycle in the forest sites, while 13C patterns suggested differences in plant water use efficiency across the C3 grassland sites. The forests and grassland sites stored the majority of surface SOC and TN in the LF and hPOM pools. Sustained sequestration of C and N in these rather labile pools will rely on management practices that minimize soil disturbance and increase C input. We also found that the mineral fraction (silt and clay) in the cropland soils stored less C and N per unit of fraction mass compared to the forests and grasslands, which points towards a lower mineral-OM stabilization efficiency of cropland soils. Finally, our study revealed total POM (LF plus hPOM) as a strong predictor of SOC and TN differences, particularly among the non-cropped sites. This study shows that these sites, independent of soil type and climate, store a large fraction of C and N in POM pools that are particularly vulnerable to soil disturbance such as caused by land use change.