The electron channeling effect, i.e., the dependence of the characteristic x-ray emission on the crystallographic direction of the incoming beam in an analytical transmission electron microscope was employed to elucidate the crystal site location and distribution of the dopant and host ions in Mg2Si1-xSnx thermoelectric (TE) materials, doped with low amounts of Bi. Experiments performed both in pure Bi-doped Mg2Si and mixed Mg2Si1-xSnx (x = 0.4, 0.6), firmly confirmed that Mg occupies the two tetrahedral T sites, 8c (¼, ¼, ¼) and (¼, ¼, ¾), with some vacancies present, too, whereas Si and Sn the 4a (0, 0, 0) and 4b (½, ½, ½) octahedral C and N sites, respectively. Bi ions follow the trend of Si and Sn, occupying 4a sites, but also there is a partial distribution of them in 4b sites. We moreover observe a certain degree of asymmetry along the {111} directions in Mg2Si1-xSnx, predominately for the variable distribution of Bi and Sn in the lattice, which indicates Bi substitution for Sn in an uneven fashion. The channeling results are in line with TE property measurements, especially in relation to lower thermal conductivity and negative Seebeck coefficient due to Bi incorporation in the lattice. These findings demonstrate once more the effectiveness of the channeling technique to provide direct crystallographic information and refine atom positions in materials, particularly for nanoscale crystal grains.