[en] The unavoidable presence of vibrations in solid-state devices can drastically modify the expected electron spin resonance (ESR) absorption spectrum in magnetically active systems. In this work, we model the effect of phonons and temperature on the ESR signal in molecular systems with strong E ⊗ e Jahn–Teller (JT) effect and an electronic spin-1/2. Our microscopic model considers the linear JT interaction with a continuum of phonon modes, the spin–orbit coupling, the Zeeman effect, and the response of the system under a weak oscillating magnetic field. We derive a Lindblad master equation for the orbital and spin degrees of freedom, where one- and two-phonon processes are considered for the phonon-induced relaxation, and the thermal dependence of Ham reduction factors is calculated. We find that the suppression of ESR signals is due to phonon broadening but not based on the common assumption of orbital quenching. Our results can be applied to explain the experimentally observed absence of the ESR signal in color centers in diamond, such as the neutral nitrogen-vacancy and negatively charged silicon-vacancy color centers in diamond. (paper)