The chemical behavior of bilayer graphene under strong covalent and non-covalent functionalization is relatively unknown compared to monolayer graphene, which has been far more widely studied. Bilayer graphene is significantly less chemically reactive than monolayer graphene, making it more challenging to study its chemistry in detail. However, bilayer graphene is increasingly attractive for electronic applications rather than monolayer graphene because of its electric field-controllable band gap, and there is a need for a greater understanding of its chemical functionalization. In this paper, we study the covalent and non-covalent functionalization of bilayer graphene using an electrochemical process with aryl diazonium salts in the high conversion regime (D/G ratio > 1), and we use Raman spectroscopic mapping and conductive atomic force microscopy (cAFM) to study the resulting changes in the physical and electronic structures. Covalent functionalization at high chemical conversion induces distinct changes in the Raman spectrum of bilayer graphene including the broadening and shift in position of the split G peak. Also, the D peak becomes active with four components. We report for the first time that the broadening of the 2D22 and 2D21 components is a distinct indicator of covalent functionalization, whereas the decrease in intensity of the 2D11 and 2D12 peaks corresponds to doping. Conductive AFM imaging shows physisorbed species from non-covalent functionalization can be removed by mechanical and electrical influence from the AFM tip, and that changes in conductivity due to functionalization are inhomogeneous. These results allow one to distinguish covalent from non-covalent chemistry as a guide for further studies of the chemistry of bilayer graphene.