Thermoelectric properties of semiconducting β-FeSi2 containing a homogeneous distribution of Si secondary phase have been studied. The synthesis was carried out using arc melting followed by the densification by uniaxial hot pressing. Endogenous β-FeSi2/Si composites were produced by the eutectoid decomposition of high-temperature α-Fe2Si5 phase. The aging heat treatments have been carried out at various temperatures below the equilibrium eutectoid temperature for various durations in order to tune the size of the eutectoid product. Thermal properties of the samples were studied in the temperature range of 100–350 °C. The microstructural investigations support the fact that the finest microstructure generated through the eutectoid decomposition of the α-Fe2Si5 metastable phase is responsible of the phonon scattering. The results suggest an opportunity to produce bulk iron silicide alloys with reduced thermal conductivity in order to enhance its thermoelectric performance.