We present a first-principles investigation of spin-phonon relaxation in a molecular crystal of Co2+ single-ion magnets. Our study combines electronic structure calculations with machine-learning force fields and unravels the nature of both the Orbach and the Raman relaxation channels in terms of atomistic processes. We find that although both mechanisms are mediated by the excited spin states, the low temperature spin dynamics is dominated by phonons in the THz energy range, which partially suppress the benefit of having a large magnetic anisotropy. This study also determines the importance of intra-molecular motions for both the relaxation mechanisms and paves the way to the rational design of a new generation of single-ion magnets with tailored spin-phonon coupling.