A-site deficient perovskites are among the most important n-type thermoelectric oxides. Ceramics of Sr1−xPr2x/3x/3TiO3 (x = 0.1 to 1.0) were prepared by solid state reaction at 1700-1723 K using highly reducing atmospheres. Samples with the highest Sr content had a cubic crystal structure (Pm3 ̅m); incorporating Pr with A-site vacancies, led to a reduction in symmetry to tetragonal (I4/mcm) and then orthorhombic (Cmmm) crystal structures. HRTEM showed Pr2/3TiO3 had a layered structure with alternating fully and partially occupied A-sites and a short-range order along (100) direction. Electrical conductivity was highest in samples of high symmetry (x ≤ 0.40), where the microstructures featured core-shell and domain structures. This enabled a very high power factor of ~1.75×10−3 W m−1 K−2 at 425 K. In contrast, at high Pr content, structural distortion led to reduced electron transport; enhanced phonon scattering (from mass contrast, local strain and cation-vacancy ordering) led to reduced, glass-like, thermal conductivity. Carbon burial sintering increased the oxygen deficiency leading to increased carrier concentration, a maximum power factor of ~1.80×10−3 W m−1 K−2 at 350 K and thermoelectric figure of merit of 0.26 at 865 K. The paper demonstrates the importance of controlling both crystal structure and microstructure to enhance thermoelectric performance.