Si-based epitaxial β-FeSi2 thin films are attractive as materials for on-chip thermoelectric power generators. We investigated the structure, crystallinity, and thermoelectric properties of β-FeSi2 thin films epitaxially grown on Si(111) substrates by using three different techniques: conventional reactive deposition epitaxy followed by molecular beam epitaxy (RDE+MBE), solid phase epitaxy (SPE) based on codeposition of Fe and Si presented previously, and SPE followed by MBE (SPE+MBE) presented newly by this work. Their epitaxial growth temperatures were fixed at 530 °C for comparison. RDE+MBE thin films exhibited high crystalline quality, but rough surfaces and rugged β-FeSi2/Si(111) interfaces. On the other hand, SPE thin films showed flat surfaces and abrupt β-FeSi2/Si(111) interfaces but low crystallinity. We found that SPE+MBE thin films realized crystallinity higher than SPE thin films, and also had flatter surfaces and sharper interfaces than RDE+MBE thin films. In SPE+MBE thin film growth, due to the initial SPE process with low temperature codeposition, thermal interdiffusion of Fe and Si was suppressed, resulting in the surface flatness and abrupt interface. Second high temperature MBE process improved the crystallinity. We also investigated thermoelectric properties of these β-FeSi2 thin films. Structural factors affecting the thermoelectric properties of RDE+MBE, SPE, and SPE+MBE thin films were investigated.