This work presents a systematic investigation of scandia alumina stabilized zirconia (ScAlSZ, composition: ZrO2:Sc2O3:Al2O3 93:6:1 wt.%) thin films (~2 μm). Thin films were formed by the e-beam evaporation method on 450 °C substrates. The influence of Al concentration on thin film microstructure, structure, and electrochemical properties was characterized by EDS, XRD, Raman, and EIS methods. It was found that the aluminum concentration in the deposited thin films decreased with an increase in the deposition rate. The concentration of Al changed from 15.9 to 3.8 at.% when the deposition rates were 0.2 and 1.6 nm/s, respectively. The crystallinity of the thin films depended strongly on the concentration of Al, resulting in an amorphous phase when Al concentration was 22.2 at.% and a crystalline phase when Al concentration was lower. ScAlSZ thin films containing 15.9 at.% of Al had monoclinic and tetragonal phases, while thin films with 1.6 and 3.8 at.% of Al had a mixture of cubic, tetragonal, and monoclinic phases. The phase transition was observed during the thermal annealing process. Cubic and rhombohedral phases formed in addition to monoclinic and tetragonal phases appeared after annealing ScAlSZ thin films containing 15.9 and 22.2 at.% of aluminum. The highest total ionic conductivity (σbulk = 2.89 Sm−1 at 800 °C) was achieved for ScAlSZ thin films containing 3.8 at.% of Al. However, thin films containing a higher concentration of aluminum had more than 10 times lower total conductivity and demonstrated changes in activation energy at high temperatures (>560 °C). Activation energies changed from ~1.10 to ~1.85 eV.