Objectives Clinical Data Warehouses (CDW) are the designated infrastructures to enable access and analysis of large quantities of electronic health record data. Building and managing such systems implies extensive “data work” and coordination between multiple stakeholders. Our study focuses on the challenges these stakeholders face when designing, operating, and ensuring the durability of CDWs for research. Materials and Methods We conducted semistructured interviews with 21 professionals working with CDWs from France and Belgium. All interviews were recorded, transcribed verbatim, and coded inductively. Results Prompted by the AI boom, healthcare institutions launched initiatives to repurpose data they were generating for care without a clear vision of how to generate value. Difficulties in operating CDWs arose quickly, strengthened by the multiplicity and diversity of stakeholders involved and grand discourses on the possibilities of CDWs, disjointed from their actual capabilities. Without proper management of the information flows, stakeholders struggled to build a shared vision. This was evident in our interviewees’ contrasting appreciations of what mattered most to ensure data quality. Participants explained they struggled to manage knowledge inside and across institutions, generating knowledge loss, repeated mistakes, and impeding progress locally and nationally. Discussion and conclusion Management issues strongly affect the deployment and operation of CDWs. This may stem from a simplistic linear vision of how this type of infrastructure operates. CDWs remain promising for research, and their design, implementation, and operation require careful management if they are to be successful. Building on innovation management, complex systems, and organizational learning knowledge will help.