The optomechanical character of molecules was discovered by Raman about one century ago. Today, molecules are promising contenders for high-performance quantum optomechanical platforms because their small size and large energy-level separations make them intrinsically robust against thermal agitations. Moreover, the precision and throughput of chemical synthesis can ensure a viable route to quantum technological applications. The challenge, however, is that the coupling of molecular vibrations to environmental phonons limits their coherence to picosecond time scales. Here, we improve the optomechanical quality of a molecule by several orders of magnitude through phononic engineering of its surrounding. By dressing a molecule with long-lived high-frequency phonon modes of its nanoscopic environment, we achieve storage and retrieval of photons at millisecond timescales and allow for the emergence of single-photon strong coupling in optomechanics. Our strategy can be extended to the realization of molecular optomechanical networks.