Nanostructured phonon-glass thermoelectric materials are highly sought after for heat waste recovery applications. This work introduces a novel phonon-glass multi-phase ceramic material synthesized from sintered mixtures of two sub-stoichiometric tungsten oxides, WO2.90 and WO2.72. Notable measurements were recorded for our sample, denoted as 0.1WO2.72/0.9WO2.90, at 800 °C, with S2σ = 0.51 ± 0.03 mWm−1K−2, representing a tenfold increase compared to the base materials. The lattice thermal conductivity, already displaying phonon-glass characteristics, is further suppressed by the addition of the secondary WO2.72 pentacolumn phase, reaching its lowest value at 0.54 ± 0.25 Wm−1K−1. As a result, the ZT value is enhanced to twice the intrinsic value of the pristine phase. This study demonstrates a novel strategy for improving the thermoelectric performance of oxide-based materials by leveraging a synergistic relationship among several key factors, including phonon-glass nanostructures, tunable electrical properties, and the reduction of lattice thermal conductivity within a homogeneous composite system.