The effects of Li deposition on hydrogenated bilayer graphene on SiC(0001) samples, i.e. on quasi-freestanding bilayer graphene samples is studied using low energy electron microscopy, micro-low-energy electron diffraction and photoelectron spectroscopy. After deposition, some Li atoms form islands on the surface creating defects that are observed to disappear after annealing. Some other Li atoms are found to penetrate through the bilayer graphene sample and into the interface where H already resides. This is revealed by the existence of shifted components, related to H-SiC and Li-SiC bonding, in recorded core level spectra. The Dirac point is found to exhibit a rigid shift to about 1.25 eV below the Fermi level, indicating strong electron doping of the graphene by the deposited Li.