BackgroundDigital transformation in healthcare and the growth of health data generation and collection are important challenges for the secondary use of healthcare records in the health research field. Likewise, due to the ethical and legal constraints for using sensitive data, understanding how health data are managed by dedicated infrastructures called data hubs is essential to facilitating data sharing and reuse.MethodsTo capture the different data governance behind health data hubs across Europe, a survey focused on analysing the feasibility of linking individual-level data between data collections and the generation of health data governance patterns was carried out. The target audience of this study was national, European, and global data hubs. In total, the designed survey was sent to a representative list of 99 health data hubs in January 2022.ResultsIn total, 41 survey responses received until June 2022 were analysed. Stratification methods were performed to cover the different levels of granularity identified in some data hubs’ characteristics. Firstly, a general pattern of data governance for data hubs was defined. Afterward, specific profiles were defined, generating specific data governance patterns through the stratifications in terms of the kind of organization (centralized versus decentralized) and role (data controller or data processor) of the health data hub respondents.ConclusionsThe analysis of the responses from health data hub respondents across Europe provided a list of the most frequent aspects, which concluded with a set of specific best practices on data management and governance, taking into account the constraints of sensitive data. In summary, a data hub should work in a centralized way, providing a Data Processing Agreement and a formal procedure to identify data providers, as well as data quality control, data integrity and anonymization methods.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12961-023-01026-1.