Spin-bearing molecules can be stabilized on surfaces and in junctions with desirable properties, such as a net spin that can be adjusted by external stimuli. Using scanning probes, initial and final spin states can be deduced from topographic or spectroscopic data, but how the system transitions between these states is largely unknown. We address this question by manipulating the total spin of magnetic cobalt hydride complexes on a corrugated boron nitride surface with a hydrogen-functionalized scanning probe tip by simultaneously tracking force and conductance. When the additional hydrogen ligand is brought close to the cobalt monohydride, switching between a correlated S = 1/2 Kondo state,where host electrons screen themagneticmoment, and an S = 1 state with magnetocrystalline anisotropy is observed. We show that the total spin changes when the system is transferred onto a new potential energy surface that is defined by the position of the hydrogen in the junction. These results show how and why chemically functionalized tips are an effective tool to manipulate adatoms and molecules and a promising new method to selectively tune spin systems.