Adsorption of organic matter and its turnover is significantly affected by the mineralogy of clays and sesquioxides in soil. Such associations between clay mineralogy and organic carbon functional groups have commonly been studied in batch or incubation experiments. This study presents in-situ measurements of the micro-scale (5 µm resolution) spatial distribution of organic carbon functional groups using synchrotron-based Fourier-Transform Infra-Red (FTIR) spectroscopy. Using integrated spectral signals in the absorbance incidental to vibrations of organic carbon bonds, we are able to infer the organic C and mineral chemistry as well as organic matter locations in the soil organo-mineral complexes. In kaolinitic Oxisols of Kenya and Brazil, we were able to relate the spatial distribution of aliphatic-C (at 2922 cm^-1) with that of surficial kaolinitic-OH (at 3687 cm^-1). Our results also clearly indicate that the resolutions of individual peak positions of aliphatic-C and kaolinitic-OH were significantly correlated (r² = 0.66-0.75). The correlation of clay minerals vibrations with aliphatic-C were less pronounced (r² = 0.51) for an Inceptisol from North-eastern United States which was dominated by illites, but more strongly correlated with aromatic-C (r² of 0.65) than for the oxisols (r² values between 0.01 and 0.3). These data provide evidence for the involvement of hydroxylated and other clay mineral surfaces and organic carbon interfaces for the adsorption of organic matter in mineral soils.