Proton conducting BaTi1-xScxO3Hx (BTS) perovskites are promising materials for proton conducting fuel cells in the intermediate temperature regime (200-600 °C). Compared to BaZrO3-based materials, BTS undergo a phase transition between the cubic perovskite structure at high doping level, and a 6H hexagonal perovskite phase a low doping level, associated with a drop in proton conductivity. In order to link the macroscopic conductivity behavior to the proton diffusion mechanisms, we aim to characterize the lattice and proton vibrational dynamics and, subsequently, the proton local environments for both the hexagonal and cubic phases. The results will be valuable not only to understand the change in behavior with the phase transition, but in a larger view, will provide insights on the effects of acceptor-doping in proton conducting perovskites over a large composition series.