Infrared (IR) microscopy in combination with X-ray microdiffraction was used as a direct (in situ) method to study the nature of organic (and mineral) components within the organic aggregates from four Chernozemic and one Podzolic-like soils from Alberta. These methods utilized thin section peels or individual aggregates and have the capability of point analysis in area of about 50–100 μm in diameter. We compared the conventional IR spectra of soil organic matter [humic acids (HA)] with those of in situ IR spectra obtained directly from aggregates. Results showed that the band at 1720 cm−1 observed in humic acid was not present in the in situ IR spectra and instead the bands at 1735 and 1785 cm−1 correlated to esters were observed. This indicates that saponification of esters occurred during the alkaline extraction of humic acid. In situ IR spectra from an unimpregnated sample also showed a strong band around 1524 cm−1 (correlated to amide II). X-ray microdiffraction analysis showed the presence of quartz and phyllosilicates in the aggregates. The method described in this study appeared to be suited to the direct investigation of soil organic matter and may provide the methodology necessary to assess the quality of organic matter. Key words: Soil organic matter aggregates, infrared microscopy, X-ray microdiffraction