The adsorption of amino acids (AAs) on minerals plays a role in the geochemical processes that determine the availability of nutrients in the environment. Histidine can be used as typical basic AA because it is frequently detected in natural waters, soils, and sediments. Herein, the pH effects and time factor were analyzed to reveal the molecular-level mechanisms of histidine adsorption on Na-montmorillonite, anatase, and goethite. Attenuated total reflectance Fourier transform infrared (ATR–FTIR) flow-cell measurements, X-ray diffraction (XRD), and density functional theory (DFT) calculations were used to determine the adsorbed species structures and the time-dependent adsorption/desorption processes. The structures of adsorbed histidine were governed by pH conditions, but were not affected by time variations. The histidine adsorbed on the minerals was in the cationic (pH 4), neutral zwitterionic (pH 7.5), and anionic (pH 10.5) forms, which was consistent with those dissolved in solution at the same pH. Adsorption on the clay mineral montmorillonite was favorable due to the dominant interlayer adsorption mechanism at pH 4 and hydrophobic attraction (external basal surface) at pH 4–10.5. Histidine adsorption on the two metal (hydr)oxides was dominated by inner-sphere surface complexation, which involved one or two O atoms of the COO− group. The adsorbed histidine was in the monodentate form on anatase and in the bidentate form on goethite.