The deactivation during the cracking of glycerol into valued chemicals and fuels has been studied under realistic FCC conditions using HZSM-5 or HY zeolite based catalysts. These catalysts suffer a severe catalyst deactivation by coke, which has been characterized quantitatively and qualitatively by TG-TPO, MS/FTIR-TPO, FTIR, 1H and 13C NMR spectroscopies. The first part of this work delves with the product distribution and deactivation of HZSM-5 zeolite based catalyst during the transformation of (pure) aqueous glycerol. The second section focuses on the product distribution and deactivation of HY zeolite based catalyst during the joint cracking of vacuum-gas-oil (VGO) with aqueous glycerol. The results show that the mechanism of deactivation during glycerol cracking, independently of the catalyst used, involves two sequential steps: (i) condensation in the exterior of the zeolite to form an oxygenated coke and (ii) dehydration and hydrogen transfer of the previous oxygenated coke to form a more aromatic one. The second step is only activated at severer conditions (t > 3 s and T > 450 °C). Co-feeding glycerol with VGO increase the yield of coke, gases and decrease the yield of gasoline (with higher octane number), while VGO only participates in the formation of aromatic coke.