The consensus for mechanisms controlling soil organic matter (SOM) persistence has shifted from traditional views based on SOM recalcitrance to a new paradigm based on SOM stabilization controlled by soil minerals and aggregates. Recent studies indicate that the origin, composition and molecular diversity of SOM are crucial to the decomposition and stabilization of SOM. However, it is not fully understood how the decomposition and stabilization of SOM are controlled at the molecular level. The objectives of this study were to investigate whether soil organic carbon (SOC) contents and mineralization are controlled by the composition, origin and molecular diversity of SOM. Soil samples were collected from contrasting bedrocks with different precipitation levels at tropical alpine grasslands of the Peruvian Andes. We applied a combination of a 76-day soil incubation experiment and pyrolysis-GC/MS assisted by thermochemolysis to investigate SOM decomposition and stabilization at the molecular level. The results indicated that soil samples with high SOC contents (92.6 ± 7.6 g kg⁻¹ soil) and low SOC mineralization had abundant derivates of lignin, polysaccharides and n-alkanes. After the incubation, we observed neither a selective decomposition of any compound groups nor a decline of molecular diversity. In contrast, soil samples with low SOC contents (30.7 ± 2.8 g kg⁻¹ soil) and higher SOC mineralization showed a depletion of plant-derived compounds, an accumulation of microbial-derived compounds and declined molecular diversity after the incubation. Furthermore, the SOC mineralization of these samples was positively correlated to the depletion of unsaturated fatty acids and the decrease in molecular diversity after the incubation. Therefore, we proposed that SOC contents and mineralization in our soils are (1) controlled by selective preservation of SOM molecular groups (e.g. plant-derived compounds), and (2) associated with changes in molecular diversity of SOM during microbial decomposition. Due to the selective preservation of organic compounds under different environmental conditions, we propose that environmental factors should be considered for the management of ecosystem services such as SOC sequestration in the studied region.