Physical separation of soil into different soil organic matter (SOM) fractions is widely used to identify organic carbon pools that are differently stabilized and have distinct chemical composition. However, the mechanisms underlying these differences in stability and chemical composition are only partly understood. To provide new insights into the stabilization of different chemical compound classes in physically-separated SOM fractions, we assessed shifts in the biomolecular composition of bulk soils and individual particle size fractions that were incubated in the laboratory for 345 days. After the incubation, also the incubated bulk soil was fractionated. The chemical composition of organic matter in bulk soils and fractions was characterized by ¹³C-CPMAS nuclear magnetic resonance spectroscopy and sequential chemical extraction followed by GC/MS measurements. Plant-derived lipids and lignin were abundant in particulate organic matter (POM) fractions of sand-, silt-, and clay-size and the mineral-bound, clay-sized organic matter. These results indicate that recent conceptualizations of SOM stabilization probably understate the contribution of plant-derived organic matter to stable SOM pools. Although our data indicate that inherent recalcitrance could be important in soils with limited aggregation, organo-mineral interactions and aggregation were responsible for long-term SOM stabilization. In particular, we observed consistently higher concentrations of plant-derived lipids in POM fractions that were incubated individually, where aggregates were disrupted, as compared to those incubated as bulk soil, where aggregates stayed intact. This finding emphasizes the importance of aggregation for the stabilization of less ‘recalcitrant’ biomolecules in the POM fractions. Because also the abundance of lipids and lignin in clay-sized, mineral-associated SOM was substantially influenced by aggregation, the bioavailability of mineral-associated SOM likely increases after the destruction of intact soil structures.