Li3Y1-xInxCl6 undergoes a phase transition from trigonal to monoclinic via an intermediate orthorhombic phase. Although the trigonal yttrium containing the end member phase, Li3YCl6, synthesized by a mechanochemical route, is known to exhibit stacking fault disorder, not much is known about the monoclinic phases of the serial composition Li3Y1-xInxCl6. This work aims to shed light on the influence of the indium substitution on the phase evolution, along with the evolution of stacking fault disorder using X-ray and neutron powder diffraction together with solid-state nuclear magnetic resonance spectroscopy, studying the lithium-ion diffusion. Although Li3Y1-xInxCl6 with x ≤ 0.1 exhibits an ordered trigonal structure like Li3YCl6, a large degree of stacking fault disorder is observed in the monoclinic phases for the x ≥ 0.3 compositions. The stacking fault disorder materializes as a crystallographic intergrowth of faultless domains with staggered layers stacked in a uniform layer stacking, along with faulted domains with randomized staggered layer stacking. This work shows how structurally complex even the "simple" series of solid solutions can be in this class of halide-based lithium-ion conductors, as apparent from difficulties in finding a consistent structural descriptor for the ionic transport.