We propose a fast and non-destructive spectroscopic method for single molecular ions that implements quantum logic schemes between an atomic ion and the molecular ion of interest. Our proposal relies on a hybrid coherent manipulation of the two-ion system, using optical or magnetic forces depending on the types of molecular levels to be addressed (Zeeman, rotational, vibrational or electronic degrees of freedom). The method is especially suited for the non-destructive precision spectroscopy of single molecular ions, and sets a starting point for new hybrid quantum computation schemes that combine molecular and atomic ions, covering the measurement and entangling steps.