Atomic force imaging and spectroscopy provide unique tools for investigating molecular interactions and dynamics in biomolecular and biomineral systems in situ. Herein, three recent examples of methods used to gain mechanistic insights into the self-assembly of protein matrices and biomolecular controls over mineral formation are reviewed. Studies of S-layer protein assembly reveal the complex nature of the nucleation and growth pathway, demonstrate the importance of kinetic traps in determining that pathway and provide quantification of the energy barriers controlling formation rates. Investigations of citrate and polypeptide modification of calcium oxalate monohydrate growth combined with molecular dynamics simulations (MD) demonstrate the importance of stereochemical matching at atomic steps on the crystal surface and establish a direct relationship between the step edge binding energies and shape modification. Measurements of step kinetics lead to detailed atomic-scale models that include both thermodynamic and kinetic effects, including time-dependent phenomena related to the multi-stage binding dynamics of polypeptide chains. Dynamic force spectroscopy measurements of binding between amelogenin peptide segments and hydroxyapatite (HAP) crystal faces, again combined with MD simulations, establish an energetic rationale for the observed c-axis elongation characteristic of HAP in tooth enamel, based on determinations of the peptide-HAP binding free energy. These examples demonstrate the deep level of understanding that can be obtained by applying in situ AFM imaging and force spectroscopy to biomolecular and biomineral systems.