We investigate transport through a mononuclear rare-earth metal-organic shell complex with strong tunnel coupling between the shell and two electrodes. The ground state of this molecule is a singlet while the first excited state is a triplet. We show that modulation of the tunnel barrier due to a molecular distortion which couples to the tunneling induces the Kondo effect, provided the discrete vibrational energy compensates the singlet/triplet gap. We discuss also the possibility of tuning the phonon-induced Kondo tunneling by external magnetic field and the finite bias Kondo anomaly.