AbstractLong residence times of soil organic matter have been attributed to reactive mineral surface sites that sorb organic species and cause inaccessibility due to physical isolation and chemical stabilization at the organic–mineral interface. Instrumentation for probing this interface is limited. As a result, much of the micron- and molecular-scale knowledge about organic–mineral interactions remains largely qualitative. Here we report the use of force spectroscopy to directly measure the binding between organic ligands with known chemical functionalities and soil minerals in aqueous environments. By systematically studying the role of organic functional group chemistry with model minerals, we demonstrate that chemistry of both the organic ligand and mineral contribute to values of binding free energy and that changes in pH and ionic strength produce significant differences in binding energies. These direct measurements of molecular binding provide mechanistic insights into organo–mineral interactions, which could potentially inform land-carbon models that explicitly include mineral-bound C pools.