Increased understanding of the stabilization mechanisms of the organic matter (OM) entering the soil system through the application of organic amendments is of paramount agronomic and environmental importance. Here, we examined the organic C and total N distribution in OM pools (i.e. free, intra-macroaggregate, intramicroaggregate, mineral-associated, dissolved, and humic acid fractions) characterized by different protection mechanisms in soils annually amended with different organic substrates of municipal origin (i.e. municipal solid waste compost, sewage sludge compost, and thermally dried sewage sludge) for three years. With respect to the unamended control soil, the application of the three organic materials, especially thermally dried sewage sludge, increased soil organic C, and total N contents. The organic inputs accumulated mostly in the physically unprotected free OM pool, as relatively fresh, low humified materials, and secondarily in the intra-macroaggregate fraction, as partially decomposed OM weakly protected by physical mechanisms. Our results suggest that mechanisms related to strong physical protection in microaggregates and chemical inaccessibility by intimate association with minerals do not govern OM stabilization in the short term.