Vibrations play a prominent role in magnetic relaxation processes of molecular spin qubits as they couple to spin states, leading to the loss of quantum information. Direct experimental determination of vibronic coupling is crucial to understand and control the spin dynamics of these nano-objects, which represent the limit of miniaturization for quantum devices. Herein, we measure the magneto-infrared properties of the molecular spin qubit system Na9[Ho(W5O18)2]·35H2O. Our results place significant constraints on the pattern of crystal field levels and the vibrational excitations allowing us to unravel vibronic decoherence pathways in this system. We observe field-induced spectral changes near 63 and 370 cm-1 that are modeled in terms of odd-symmetry vibrations mixed with f-manifold crystal field excitations. The overall extent of vibronic coupling in Na9[Ho(W5O18)2]·35H2O is limited by a modest coupling constant (on the order of 0.25) and a transparency window in the phonon density of states that acts to keep the intramolecular vibrations and MJ levels apart. These findings advance the understanding of vibronic coupling in a molecular magnet with atomic clock transitions and suggest strategies for designing molecular spin qubits with improved coherence lifetimes.