Light fraction (LF) and permanganate-oxidizable C (POXC) demonstrate high reliability as indicators for monitoring soil functioning in response to changes in soil organic carbon (SOC). However, mechanisms affecting the amount and composition of labile fractions and their relationship with SOC content at regional scales have not been thoroughly studied. The aim of this study was to examine the spectral features associated with these labile organic matter fractions in samples collected from 75 sites under different soil types, land use and climatic conditions in Chile. Topsoil was analyzed for total C and N content, aggregate stability, and texture. Additionally, the spectral properties of LF material and whole soils were analyzed using diffuse reflectance mid-infrared spectroscopy (MidIR). Our results show that LF shared a similar spectral composition but with different band intensities across climatic regimes. LF spectra were associated with O-alkyl C in cool and rainy areas, whereas a relative accumulation of aromatic structures was found in warmer areas. Whole soils spectra showed that SOC, POXC and aggregability were related to the prevalence of aliphatic and polysaccharides compounds in colder areas. While in warm arid areas, the stabilization of aliphatic compounds was found to be related to clay minerals. Furthermore, we found that POXC and SOC content were closely related and changes in POXC were affected by variations in climate conditions. The understanding of spectral features linked to labile SOC fractions on at larger geographical scale will contribute to the development of sustainable land management options for the prevention of land degradation in the context of adaptation to climate change.