Purpose This study aims to further the understanding of multi-level analysis in inter-organisational relationships by investigating the interplay of governance, cooperation and coordination in inter-organisational projects (IOPs) on sub-system and project levels. Design/methodology/approach The authors use the Viable Systems Model as a framework to analyse inter-organisational project governance, cooperation and coordination by adopting a multiple-case study. Findings The findings illustrate how governance and coordination mechanisms exhibit a filter-down effect on lower sub-systems while cooperation influence is confined within each sub-system. While remarking the importance of specific sub-systems on the overall project performance, the interplay of governance, cooperation and coordination across sub-systems appears to be complex, with governance influencing cooperation and coordination, whereas cooperation and coordination influence each other with an incremental effect. Originality/value This study defines two propositions that explain how multiple levels of analysis (project and sub-systems) can support the governance of large inter-organisational projects. The authors elaborate theory on the interplay of inter-organisational project governance, cooperation and coordination.