The development of spin qubits for quantum technologies requires their protection from the main source of finite-temperature decoherence: atomic vibrations. Here we eliminate one of the main barriers to the progress in this field by providing a complete first-principles picture of spin relaxation that includes up to two-phonon processes. Our method is based on machine learning and electronic structure theory and makes the prediction of spin lifetime in realistic systems feasible. We study a prototypical vanadium-based molecular qubit and reveal that the spin lifetime at high temperature is limited by Raman processes due to a small number of THz intra-molecular vibrations. These findings effectively change the conventional understanding of spin relaxation in this class of materials and open new avenues for the rational design of long-living spin systems.