Metal-doped iron silicides (β-FeSi2) are promising thermoelectric materials for high-temperature applications. However, the addition of metal dopants usually causes the formation of secondary metallic phases, resulting in the degradation of thermopower. Here we report the stability of semiconducting β-phase (higher than 95 %) of Mn-doped β-FeSi2 obtained at Mn concentration from 1 % to 5 %, where the samples were prepared through direct arc melting and heat treatment process. The carrier density remarkably increases with Mn content, but the mobility decreases. The electrical resistivity significantly decreases with Mn content. The Seebeck coefficient of Mn-doped samples is improved and stable at high-temperature regions because of the reduction of the bipolar effect and β-phase stability. The thermal conductivity slightly increases with Mn. As a result, the maximum thermoelectric power factor PF = 970 μWm−1K−2 and dimensionless figure of merit ZT = 0.12 at 800 K are obtained in a 3 % Mn-doped sample. The stability of β-phase and the improved carrier density are the origins of enhanced thermoelectric properties, where the Seebeck coefficient is improved, and the electrical resistivity is reduced. Our study provides insight into the importance of phase stability for enhancing thermoelectric transport in Mn-doped β-FeSi2.