In recent years, layered chalcogenides have attracted interest for their appealing thermoelec- tric properties. We investigated the Ge2Sb2Te5 compound in two different stacking sequences, named stacking 1 (S1) and stacking 2 (S2), wherein the Ge and Sb atomic positions can be interchanged in the structure. The compound unit cell, comprising nine atoms, is made of two layers separated by a gap. We show, using the quantum theory of atoms in molecules, that the bonding across the layers has characteristics of transit region bonding, though with a close resemblance to closed-shell bonding. Both S1 and S2 are shown to bear a similar small gap. The full determination of their thermoelectric properties, including the Seebeck coefficient, electrical conductivity and electronic and lattice thermal conductivities, was carried out by solving the Boltzmann transport equation. We show that stacking 1 exhibits a larger Seebeck coefficient and smaller electrical conductivity than stacking 2, which is related to their small electronic gap difference, and that S1 is more suitable for thermoelectric application than S2. Moreover, under certain conditions of temperature and doping level, it could be possible to use S1-Ge2Sb2Te5 as both a p and n leg in a thermoelectric converter. Under biaxial, tensile and compressive strains, we observe that the thermoelectric properties are improved for both S1 and S2. Furthermore, the increase in the power factor of S1 in the cross-plane direction, namely perpendicular to the gap between the layers, shows that strains can counteract the electronic transport hindrance due to the gap.