Abstract Hybrid atom-ion systems are a rich and powerful platform for studying chemical reactions, as they feature both excellent control over the electronic state preparation and readout as well as a versatile tunability over the scattering energy, ranging from the few-partial wave regime to the quantum regime. In this work, we make use of these excellent control knobs, and present a joint experimental and theoretical study of the collisions of a single 138Ba+ ion prepared in the 5d 2D3/2,5/2 metastable states with a ground state 6Li gas near quantum degeneracy. We show that in contrast to previously reported atom-ion mixtures, several non-radiative processes, including charge exchange, excitation exchange and quenching, compete with each other due to the inherent complexity of the ion-atom molecular structure. We present a full quantum model based on high-level electronic structure calculations involving spin-orbit couplings. Results are in excellent agreement with observations, highlighting the strong coupling between the internal angular momenta and the mechanical rotation of the colliding pair, which is relevant in any other hybrid system composed of an alkali-metal atom and an alkaline-earth ion.