Thermoelectric materials are expected to become new alternative sources of sustainable energy. Among them, the SnSe intermetallic alloy has been described as an excellent thermoelectric compound, characterized by an extremely low thermal conductivity with maximum performance at the onset of a structural phase transition at 800K. Recently, novel SnSe derivatives with Ge substitution have been synthesized by a direct arc-melting technique. This produces nanostructured polycrystalline samples that exhibit a record high Seebeck coefficient, anticipating an excellent performance above room temperature. Here, the structural phase transition from a GeS-type structure (space group Pnma) to a TlI-type structure (space group Cmcm) is investigated in situ via neutron powder diffraction (NPD) in the temperature range 298-853K for the selected composition Sn0.8Ge0.2Se. This transition takes place at 803K, as shown by differential scanning calorimetry. The analysis from the NPD data shows a non-monotonic behaviour of the anisotropic displacement parameters upon entering the domain of the Cmcm structure. The energies of the atomic vibrations have been quantitatively analysed by fitting the temperature-dependent mean-square displacements to Einstein oscillators. The thermal conductivity of Sn0.8Ge0.2Se is as low as 0.35Wm(-1)K(-1) at 773K, which mostly represents the lattice thermal contribution.