Recent research and practice point out to interoperable logistics as the future of system communication in the transport and logistics (T&L) sector. The concept of system federation has been found to foster and accelerate the transition to seamless T&L operations. System federation has been implemented in three multimodal cases in Greece: Port-to-rail international transport, Port-to-road domestic transport, and Vessel-Road-Rail cargo bundling. This paper employs a multiple case study approach to analyze digitalization gaps and federation implementation best practices. As a general conclusion, system federation and digitalization of data exchange interfaces enhanced real-time track and tracing of shipments, as well as the communication between the involved actors in the areas of concern – and especially at the multimodal interfaces where system interoperability has been generally low.