Addressing the role of quantum coherence in the interplay between the different matter constituents (electrons, phonons and spin) is a critical step towards understanding transition metal oxides and design complex materials with new functionalities. Here we use coherent vibrational control of onsite d-d electronic transitions in a model edge-sharing insulating transition metal oxide (CuGeO3) to single-out the effects of vibrational coherence in electron-phonon coupling. By comparing time domain experiments based on high and low frequency ultrashort pumps with a fully quantum description of phonon assisted absorption, we could distinguish the processes associated to incoherent thermal lattice fluctuations from those driven by the coherent motion of the atoms. In particular, while thermal fluctuation of the phonon bath uniformly increases the electronic absorption, the resonant excitation of phonon modes results also in light-induced transparency which is coherently controlled by the vibrational motion.