Nanostructured β-FeSi2 and β-Fe0.95Co0.05Si2 specimens with a relative density of up to 95% were synthesized by combining a top-down approach and spark plasma sintering. The thermoelectric properties of a 50 nm crystallite size β-FeSi2 sample were compared to those of an annealed one, and for the former a strong decrease in lattice thermal conductivity and an upshift of the maximum Seebeck’s coefficient were shown, resulting in an improvement of the figure of merit by a factor of 1.7 at 670 K. For β-Fe0.95Co0.05Si2, one observes that the figure of merit is increased by a factor of 1.2 at 723 K between long time annealed and nanostructured samples mainly due to an increase in the phonon scattering and an increase in the point defects. This results in both a decrease in the thermal conductivity to 3.95 W/mK at 330 K and an increase in the power factor to 0.63 mW/mK2 at 723 K.