Most of the organic C in a wide range of soils is associated with mineral colloids. There are distinct interactive mechanisms between soil minerals and organic matter. Metal oxides are ubiquitous in soils and play a very significant role in influencing soil behavior and the impact on the ecosystem. Biomolecules exert a very significant influence on the formation and transformation of Al and Fe oxides and the resultant alteration of their surface properties pertaining to the speciation, fate and bioavailability of nutrients, and toxic inorganic and organic substances. Different biomolecules substantially differ in their ability to perturb the crystallization of these oxides, enhance their specific surface area, and decrease their point of zero charge (pzc), which are evidently related to the chemical affinity of biomolecules to Al and Fe. More recent studies show that the presence of organics such as tannate during the formation of Al hydroxides triggers the formation of microporosity, decreases the average pore size, and enhances the micropore specific surface area through structural perturbation. Humic substances are formed through biotic and abiotic processes. A variety of biomolecules, such as carbohydrates, phenolic compounds, and amino acids, can participate as raw materials. Soil mineral surfaces play a vital role in the catalysis of abiotic formation of humic substances. Both the Maillard reaction and the polyphenol polymerization model are considered as separate significant pathways for the formation of humic polycondensates. More recent research findings point to a linking of the polyphenol and Maillard reactions under mineral catalysis in humification pathways, which is a significant advancement in the understanding of humification processes in the environment. Most of the chemically stabilized organic C in soils is degraded slowly on timescales from centuries to millennia. The interaction of Al and Fe with organic substances is of primary importance in the determination of the content of organic matter in tropical and temperate soils. The amount of C stabilized per unit weight of mineral is much greater for noncrystalline than for crystalline minerals. A positive relationship between noncrystalline minerals and organic C exists in soils through the climate gradient. Noncrystalline minerals can retard the organic matter from being biodegraded, which in turn, inhibits the transformation of noncrystalline mineral phases into more stable crystalline minerals. Therefore, soil mineral-organic matter interactions are important in determining the quantity of organic matter stored in soil, its turnover time, and atmosphere-ecosystem carbon flux during long-term soil development.