On 11 June 2019, two Interoperability European Union (EU) Regulations entered into force. With it, six existing EU databases created for security and border management purposes merged into one single, overarching EU information system operating with the purpose of changing the way front-line officers worked in various tasks. The main objective of these Regulations was to prevent and combat illegal immigration and to improve security within the Area of Freedom, Security and Justice of the Union. This article studies the challenges that have emerged from making EU databases and information systems ‘interoperable’ as well as the potential negative consequences that the Regulations may have for fundamental rights as enshrined in the EU Charter of Fundamental Rights. In particular, it examines whether the interoperability between EU information systems could violate the rights related to data protection, rights of the child, prohibition of discrimination as well as principles of necessity and proportionality.