Recent studies show increasing evidence for perseveration of soil organic matter (SOM) controlled by interactions with the soil matrix (i.e. mineral surfaces and aggregates) rather than chemical recalcitrance of the SOM. However, a consensus is still absent for potential controls of SOM chemical composition on SOM stabilization and persistence. Soil fatty acids (FAs), which form an important SOM component, can be used to investigate the effects of chemical properties on SOM stabilization because they are easily degraded by microorganisms but can be stabilized by the soil matrix against decomposition. Here we investigated whether inherent molecular properties of FAs control their stability in soils and their interactions with the soil matrix. Soil samples were collected from alpine grasslands of the Peruvian Andes (Andosols, Umbrisols and Phaeozems), as they are characterized by high carbon stocks and abundant aliphatics. We applied pyrolysis - gas chromatography/mass spectrometry analyses assisted by tetramethylammonium hydroxide (TMAH-pyrolysis-GC/MS) to determine the chemical composition of bulk SOM and FAs before and after a 76-day incubation experiment, comparing a situation with intact versus crushed soil aggregates. The results showed that the TMAH-pyrolysis-GC/MS yielded a large proportion of FAs (>60% relative abundance of identified compounds), with a major contribution of free FAs. FA stability was controlled by the presence of double bonds (unsaturated vs. saturated FAs) and carbon chain length. Unsaturated FAs significantly (P < 0.05) predicted soil organic carbon mineralization rates and were more depleted after the incubation compared to saturated FAs. The depletion of unsaturated FAs is likely explained by their easier degradation compared to saturated FAs. The easier degradation might be explained by the smaller extent of stabilization through association with mineral surfaces and/or chemical properties rather than stabilization through occlusion in aggregates. In terms of carbon chain length, FA stability decreased from short-chain to long-chain FAs. A possible explanation for this is that short-chain FAs received more protection by occlusion in aggregates compared to long-chain FAs or that short-chain FAs were produced during the incubation as a result of microbial transformation of FAs. Such microbial transformation has limited effects on the prediction of FA stability using double bonds and carbon chain length. However, we observed that soil types and horizons did influence the controls of double bonds and carbon chain length on FA stability. Our results corroborate the hypothesis that the inherent properties of soil FAs control their interactions with the soil matrix and indirectly govern their stabilization and persistence in the Peruvian Andean soils under study.