AbstractSpin‐crossover compounds can be switched between two stable states with different magnetic moments, conformations, electronic, and optical properties, which opens appealing perspectives for technological applications including miniaturization down to the scale of single molecules. Although control of the spin states is crucial their direct identification is challenging in single‐molecule experiments. Here we investigate the spin‐crossover complex [Fe(HB(1,2,4‐triazol‐1‐yl)3)2] on a Cu(111) surface with scanning tunneling microscopy and density functional theory calculations. Spin crossover of single molecules in dense islands is achieved via electron injection. Spin‐flip excitations are resolved in scanning tunneling spectra in a magnetic field enabling the direct identification of the molecular spin state, and revealing the existence of magnetic anisotropy in the HS molecules.