Detecting coherent phonons pose different challenges compared to coherent photons due to the much stronger interaction between phonons and matter. This is especially true for high frequency heat carrying phonons, which are intrinsic lattice vibrations experiencing many decoherence events with the environment, and are thus generally assumed to be incoherent. Two photon interference techniques, especially coherent population trapping (CPT) and electromagnetically induced transparency (EIT), have led to extremely sensitive detection, spectroscopy and metrology. Here, we propose the use of two photon interference in a three-level system to sense coherent phonons. Unlike prior works which have treated phonon coupling as damping, we account for coherent phonon coupling using a full quantum–mechanical treatment. We observe strong asymmetry in absorption spectrum in CPT and negative dispersion in EIT susceptibility in the presence of coherent phonon coupling which cannot be accounted for if only pure phonon damping is considered. Our proposal has application in sensing heat carrying coherent phonons effects and understanding coherent bosonic multi-pathway interference effects in three coupled oscillator systems.