Abstract Background The maritime sector is exposed to specific risks in the area of communicable diseases. In Germany, five ports are designated to enforce the International Health Regulations (IHR) and must have certain core capacities to respond immediately to cross-border health threats. A joint external evaluation conducted by the World Health Organization (WHO) revealed a need to reinforce central structures in Germany. The overarching objective of the study is to harmonize and consolidate the requisite capacities for maritime health security. Methods Qualitative interviews (n = 35) at baseline were conducted with various stakeholders, including port medical services, port authorities and other stakeholders. The parameters to be analysed included specific activities and interfaces during infectious incidents, experience with past infection incidents, training and exercise, and the need for action. Furthermore, a document analysis was conducted, during which the existing contingency plans and standard operating procedures were reviewed. Results In essence, the initial challenges posed by the COVID-19 pandemic have led to the establishment of well-defined procedures and interfaces between the various stakeholders involved. There is a necessity for enhanced interpersonal communication between the various stakeholders and the implementation of sustainable training practices. Furthermore, greater transparency and standardisation of regulations in international health emergencies is desired. Conclusions Given the infrequency of cross-border infection incidents on board ships, targeted preparation within stakeholders is often given a lower priority than other work priorities. The participatory study design is intended to develop comprehensive concepts in collaboration with the IHR ports in the ongoing project. Subsequently, these concepts will be tested in tabletop exercises and incorporated into training formats for public health actors. Key messages • The qualitative interview study at baseline revealed a substantial need for sustained communication and training practices among stakeholders for infectious disease preparedness in German IHR ports. • The document analysis revealed relevant differences in the extent and scope of contingency plans of German ports designated under the International Health Regulations.