The European Union Agency for the Operational Management of Large-Scale IT Systems in the Area of Freedom, Security, and Justice (eu-LISA) has been delegated the implementation of large-scale IT systems as well as their forthcoming interoperability. As such, the agency is entrusted with computer engineering tasks and it is involved in processing operations of individuals’ personal data, especially migrants. This agency is assigned crucial tasks in the design, development, and monitoring phases of interoperability components and participates in the decision-making process establishing the means for processing personal data. This post sheds light on the agency’s involvement in implementing the interoperability framework and illustrates existing challenges in allocating data processor rather than data controller responsibility.