The recent interest in the halide-based solid electrolytes Li<sub>3</sub>MX<sub>6</sub> (M = Y, Er, In; X = Cl, Br, I) shows these materials to be promising candidates for solid-state battery application, due to high ionic conductivity and large electrochemical stability window. However, almost nothing is known about the underlying lithium sub-structure within those compounds. Here, we investigate the lithium sub-structure of Li<sub>3</sub>YCl<sub>6</sub> and Li<sub>3</sub>YBr<sub>6</sub> using temperature-dependent neutron diffraction. We compare compounds prepared by classic solid-state syntheses with a mechanochemical synthesis to shed light on the influence of the synthetic approach on the reported yttrium disorder and the resulting surrounding lithium sub-structure. This work provides a better understanding of the strong differences in ionic transport depending on the synthesis procedure of Li<sub>3</sub>MX<sub>6</sub>.