New supply chain governance models transform operations by establishing large-scale, intelligent infrastructures that merge, objects, data and business processes. Considering that supply chains are intricate structures encompassing multifaceted operations, evaluating the consequences of their digital transformation is imperative. System Federation has emerged as an enabler of interoperability and seamless data exchange in transport and logistics. The Federation is a promising concept that is still new and tested only in a few instances, while; its impact has yet to be measured substantially. This paper presents the impact of Federation on the performance of selected logistics operations in Greece and Italy. Using a mixed-methods approach, the assessment performed as part of the FENIX project, focusing on operational performance, cost-effectiveness and gap analysis, and impact assessment. Results showed that the Federation showed promising overall impact. Operational improvements ranged from better shipment visibility, shorter waiting times, faster deliveries, to less CO2 emissions. The most effective services were related to a higher visibility of shipments (Italy) and improved notification and exchange of customs documents (Greece). The gap analysis was successful showing that 100% of all reported gaps in Greece and 71% in Italy could be closed with the use of the Federation.