In 2019, the European Food Safety Authority (EFSA) and the European Centre for Disease Prevention and Control (ECDC) received a mandate from the European Commission (EC) to implement and manage two interoperable systems for the collection and analysis of Whole Genome Sequence (WGS) data of Salmonella enterica, Listeria monocytogenes and Escherichia coli, including Shiga toxin‐producing E. coli (STEC) from humans and from food, feed, animals and the related environment, to contribute to the epidemiological investigations of food‐borne outbreaks and to the identification of emerging health threats. As response to this EC mandate, EFSA has developed the EFSA One Health WGS System that interoperates with the ECDC Molecular Typing system exchanging core genome Multi Locus Sequence Typing (cgMLST) profiles and minimum metadata. Interested European Union (EU) Member States (MS) and European Economic Area (EEA) countries can submit their typing data from food, feed and animal samples to the EFSA One Health WGS system either through an user‐friendly interface or programmatically. This technical report describes the EFSA One Health WGS system, including his architecture, the users and their relative data visibility, as well as data ownership and intellectual property. This report provides also detailed information on the types and formats of data that can be submitted to the EFSA One Health WGS system. Moreover, these guidelines describe the individual steps of the reporting procedure in order to support the EU MSs and EEA countries in data submission and data management.