The EOSC-ENTRUST project aims to create a European network of Trusted Research Environments (TREs) for sensitive data and drive European interoperability through the development of a common blueprint for federated data access and analysis. EOSC-ENTRUST has four drivers, or use cases, which are prototypic for federated, multinational use of TREs in research practice across scientific domains and user communities. Driver 3 demonstrates the potential ability of the blueprint to bridge the traditionally very separated data domains of clinical trials and real-world health data in one solution architecture. The present document is the protocol of the prototype for EOSC-ENTRUST Driver 3, utilising individual participant data (IPD) from a randomized controlled trial (RCT) hosted in crDSR (TSD TRE), along with real-world data (RWD) hosted in the Health Informatics Centre (HIC), University of Dundee TRE with the aim of comparing comorbidities in older adults vaccinated against COVID-19.