Understanding the effect of vibrations on the relaxation process of individual spins is crucial for implementing nano systems for quantum information and quantum metrology applications. In this work, we present a theoretical microscopic model to describe the spin-lattice relaxation of individual electronic spins associated to negatively charged nitrogen-vacancy centers in diamond, although our results can be extended to other spin-boson systems. Starting from a general spin-lattice interaction Hamiltonian, we provide a detailed description and solution of the quantum master equation of an electronic spin-one system coupled to a phononic bath in thermal equilibrium. Special attention is given to the dynamics of one-phonon processes below 1 K where our results agree with recent experimental findings and analytically describe the temperature and magnetic-field scaling. At higher temperatures, linear and second-order terms in the interaction Hamiltonian are considered and the temperature scaling is discussed for acoustic and quasi-localized phonons when appropriate. Our results, in addition to confirming a $T^5$ temperature dependence of the longitudinal relaxation rate at higher temperatures, in agreement with experimental observations, provide a theoretical background for modeling the spin-lattice relaxation at a wide range of temperatures where different temperature scalings might be expected.