Microscale interactions between mineral and chemically stable organic matter are not well resolved owing to the disruptive nature of existing soil analyses techniques. The use of bright light (> 100×) over thermal infrared sources, coupled to microscopy, now provide analytical capabilities for the in situ examination of microstructures in soil aggregates. We have used synchrotron FT-IR (Fourier Transform-Infrared) spectromicroscopy to study microscale spatial variability in the C and clay mineral complex of soil microaggregates from a tropical soil. Our objective was to elucidate C stabilization on mineral surfaces in the microstructure of the organomineral assemblage. Mapping the chemical profile of organic matter and clay mineral on ~1 µm thin sections, was achieved by illuminating the microaggregate surface regions with a 49 µm² aperture IR beam using Swarchzchild objectives, mounted on a Spectra Tech Continµm IR microscope that was connected to a Nicolet Magna 860 Spectrometer (NSLS, Brookhaven, NY, USA, Beamline U10B). Spectra were collected in transmission mode using Atlµs software. Surface area C and mineral composition maps were extracted from the integrated spectral intensity signal, at a spatial diffraction limit of ~5 µm. Bond assignments to C and OH functional group chemistry were inferred from known vibrational fingerprints in the mid infrared region (650-4000 cm^-1). Stretching vibrations of bound and non-bound OH showed that kaolinite (3696 cm^-1, 3648 cm^-1, 3620 cm^-1) and gibbsite (3520 cm^-1, 3440 cm-1) were the predominant secondary minerals forming interactions with microaggregate organic matter. Ratio intensity maps and spectra of mineral location and C functional group chemistry show evidence of a clay mineral to hydroxyl (OH) dependent mechanism for binding oxidized C to hydroxylated surfaces. Oxidized polysaccharide C forms (950-1120 cm^-1) were unevenly distributed throughout the microaggregate structure. Chemigram profiles pointed to a patchy, non-ordered location of aliphatic and aromatic C forms exhibiting strong absorbance in ~2900 cm^-1 and 1650 cm^-1 (amide I) to 1540 cm^-1 (amide II) band regions. These C forms had spectral signatures characteristic of microbial but not particulate light fraction organic matter and they appear not bound to mineral surfaces probably due to the absence of hydroxyl (OH) termini. Our data show that clay mineral binding of organic matter is primarily restricted by interactions between hydroxyl termini of oxidized C and hydroxylated/dehydroxylated mineral surfaces.