The solid solution In2−xSnxCo3S2 is attractive due to a variety of interesting properties depending on the In/Sn content, i.e. half metal ferromagnetic Sn2Co3S2, low dimensional metal In2Co3S2, and semiconducting thermoelectric InSnCo3S2. For the latter, crystal structure effects and a metal to insulator transition are not only related to electron counting but also to ordering of In and Sn within and between Co Kagomé nets. These observations have not been adequately understood to date. The degree of ordering is now evaluated from neutron diffraction data to distinguish In and Sn. The origin and effects on crystal and electronic structures are studied by DFT calculations on a superstructure model. Relations of local bonding (electron localization function ELF and Bader's AIM theory), In/Sn site preference, crystal structure distortions, and the opening of the gap are explored. Results are generalised from predictions on isoelectronic compounds.