The efficient evaluation of the transport sector for the implementation of sustainable mobility solutions is a crucial challenge for governments and decisionmakers for strategically reducing the negative economic, social, and environmental impacts of transport. Current research trends on transport macromanagement indicate a lack of integrative and comprehensive approaches to mitigating transport sustainability parameters. Thus, a holistic perspective on transport macromanagement is deemed necessary for supporting the transition towards a more sustainable approach to transport macroplanning. This paper contributes to the development of transport macromanagement by offering insights, tools, and strategies for contemporary sustainable transitions in the transport sector. A methodology for sustainable and multimodal/cross-border passenger services for the Italy-Croatia cross-border area, with a systematic development cycle composed of six interconnected steps for fostering stakeholder cooperation, is proposed in this paper. Furthermore, a methodological framework, a SWOT analysis, and a gap analysis on the function of defining port improvement for the action plan are elaborated in this study. The study analysis is based on the international passenger terminal ports in a passenger liner service by using a survey analysis conducted among the port authorities in the cross-border area. Moreover, the main aim of the methodology is to provide a holistic framework for the sustainable development of a complex and multilayered transport environment that encompasses a multiplicity of various stakeholders.