A growing field of applications for transport models is the exploration of the impact of innovations. All too often however, innovations are modelled simplistically, usually as mere reductions in transport times or costs, disregarding the related reorganization of logistics processes. In this chapter we introduce a new modelling framework for freight transport innovations that helps to fill this gap, by representing transport systems as business ecosystems. We explain the antecedents of the framework, propose an approach for its implementation using agent-based modelling, and illustrate its use in concrete cases for the area of urban freight transport. The proposed framework allows to identify stakeholders' issues and allows them to participate in designing and implementing the innovation, leading to recommendations for modelling for practitioners and researchers. Even though our scope of applications here is limited to urban freight transport, the reasoning is generic and can be also extended to passenger transport systems.