Alpine grasslands of the Neotropical Andes have high soil organic carbon (SOC) stocks and provide crucial ecosystem services. However, stability of the SOC in these grasslands is not well-studied. Having insights into SOC stability contributes to a better understanding of ecosystem vulnerability and maintaining of ecosystem services. The objectives were to get a first insight into organic matter (OM) stabilization in soils from different bedrocks of Andean alpine grasslands near Cajamarca, Peru (7° 11″ S, 78° 35″ W) and how this controls SOC stocks. Samples were collected from soils formed on limestone and acid igneous rocks. Stabilization mechanisms of OM were investigated using selective extraction methods separating active Fe, Al and Ca fractions and determined SOC stocks. In both soil types, the results showed important contributions of complexation with and/or adsorption on Fe and Al (oxides) to OM stabilization. Exclusively in the limestone soils, Ca induced OM stabilization by promoting the formation of Ca2+ bridges between OM and mineral surfaces. Furthermore, no evidence showed that OM stabilization was controlled by crystalline Fe oxides, clay contents, allophones, Al toxicity or aggregate stability. Limestone soils had significantly higher SOC stocks (405 ± 42 Mg ha−1) compared to the acid igneous rock soils (226 ± 6 Mg ha−1), which is likely explained by OM stabilization related to Ca2+ bridges in addition to the stabilization related to Fe and Al (oxides) in the limestone soils. Our results suggest a shift from OM stabilization dominated by Fe and Al (oxides) to that with the presence of Ca-related cation bridges, with increasing pH values driven by lithology.