Soil management systems that encourage the formation and stabilization of recalcitrant clay–humic complexes will have the greatest long-term impact on C sequestration and soil quality. The objective of this study was to determine the relationship between the chemical, biochemical, and spectroscopic characteristics of humic substances and clay mineralogy. Clay–humic complexes were separated from the Ap horizon of a Webster soil (fine-loamy, mixed, superactive Typic Endoaquoll) by an invasive sonication–centrifugation technique. The samples were analyzed for mineralogy by XRD (x-ray diffraction), chemical composition by inductively coupled plasma-atomic emission spectorscopy (ICP-AES), C and N by thermal combustion, C chemistry by solid state 13C magic angle spinning-nuclear magnetic resonance spectroscopy (MAS-NMR) and both gas chromatography (GC) and high performance liquid chromatography (HPLC) analyses of extractable organic compounds. The coarse, medium, and fine clay fractions are dominated by quartz, a low-charged interstratified phase, and smectite, respectively. Extractable organic compounds, 30 to 52% of the total C, are dominated by basic amino acids and polyunsaturated fatty acids. Less than 3% of the extractable C is monosaccharides and amino sugars and only trace levels of phenolic acids were found. The C/N ratios of humic substances associated with the coarse, medium, and fine clay fractions are 17, 10, and 10, respectively. The coarse clay fraction has stronger carboxyl and O-alkyl 13C-NMR peaks and lower levels of extractable amino acids, fatty acids, monosaccharides, and amino sugars than humics associated with the fine clay fraction. The results indicate that the biochemistry of the clay–humic complexes differs substantially from that of whole soils and that soil clay mineralogy strongly influences humification.