The Physical Internet (PI) is a paradigm-changing and technology-driven vision, which is expected to significantly impact the development of the freight transport and logistics (FTL) system of today. However, the development of the FTL system towards the PI creates much uncertainty for its current stakeholders. Ports are one of those stakeholders that are expected to be profoundly affected by these developments. However, research that focuses on port policy, under the uncertain developments towards the PI, is still lacking. By providing port authorities with insights and recommendations on robust policy areas, we address this void in literature. We conduct a scenario analysis in combination with multi-criteria decision analysis (MCDA) to determine the importance of port performance indicators and policy areas in different scenarios. The most significant, uncertain, and orthogonal factors for the development of the PI are technological development and institutional development. We find that for a proper alignment with the PI vision, in three out of four scenarios, ports should prioritize the implementation of digital solutions and standards, as opposed to an infrastructure focused policy.