The magnetic properties of transition-metal ions are generally described by the atomic spins of the ions and their exchange coupling. The orbital moment, usually largely quenched due the ligand field, is then seen as a perturbation. In such a scheme, S = 1/2 ions are predicted to be isotropic. We investigate a Co(II) complex with two antiferromagnetically coupled 1/2 spins on Au(111) using low-temperature scanning tunneling microscopy, X-ray magnetic circular dichroism, and density functional theory. We find that each of the Co ions has an orbital moment comparable to that of the spin, leading to magnetic anisotropy, with the spins preferentially oriented along the Co–Co axis. The orbital moment and the associated magnetic anisotropy is tuned by varying the electronic coupling of the molecule to the substrate and the microscope tip. These findings show the need to consider the orbital moment even in systems with strong ligand fields. As a consequence, the description of S = 1/2 ions becomes strongly modified, which have important consequences for these prototypical systems for quantum operations.