We theoretically investigate the transport properties of a molecule embedded in one arm of a mesoscopic Aharonov-Bohm interferometer. Due to the presence of phonons the molecule level position (εd) and the electron-electron interaction (U) undergo a polaronic shift, which affects dramatically the electronic transport through the molecular junction. When the electron-phonon interaction is weak the linear conductance presents Fano-line shapes as long as the direct channel between the electrodes is opened. The observed Fano resonances in the linear conductance are originated from the interference between the spin Kondo state and the direct path. For strong enough electron-phonon interaction, the electron-electron interaction is renormalized toward negative values, i.e., becomes effectively attractive. This scenario favors fluctuations between the empty and doubly occupied charge states and therefore promotes a charge Kondo effect. However, the direct path between the contacts breaks the electron-hole symmetry, which can efficiently suppress this charge Kondo effect. Nevertheless, we show that a proper tuning of the gate voltage is bale to revive the Kondo resonance. Our results are obtained by using the Numerical Renormalization approximation to compute the electronic spectral function and the linear conductance.