The interdependencies between infrastructures are growing. Engineering decision making that earlier was largely confined to a specific sector now requires more and more understanding of how systems interact: a system-of-systems perspective. The article analyzes the effect of that added complexity in a single case study in de Zuid-As, Amsterdam, in the Netherlands, and relates the findings to the literature on engineering decision making and project management in complex projects. The article concludes that cross-sectoral engineering decision making has an additional level of complexity that requires governance of uncertainty. Despite this challenge being a well-known challenge among infrastructure operators, it is still not recognized for its importance, and it seems to be a neglected element in collaboration. Key is an open approach in the early stages that goes beyond classic cooperative decision making in engineering and project management environments.