Jonathan became Director for Competition Policy at the Directorate-General for Competition in 1995, Deputy Director-General in charge of State aid in 1999 and Spokesman and Director-General of Press and Communication in 1999. He was Director-General of Justice and Home Affairs (later Justice, Freedom and Security) from 2003 to 2010 and then Director-General in charge of Financial Stability, Financial Services and Capital Markets Union (FISMA) between 2010 and 2015. Latterly he has served as Director-General of the Task Force for Strategic Issues related to the UK Referendum.
He studied law at the University of Sussex and has an MA from the College of Europe in Bruges. He has been a visiting lecturer at Sciences Po, a visiting fellow of the University of Cambridge Centre for European Legal Studies, a visiting professor at the College of Europe since 2009 and Emeritus Professor of Law at the Free University of Brussels (VUB) since 1989. He is a visiting Professor at King's College, London and a member of the boards of the Jacques Delors Institute in Paris and the Centre for European Reform in London. Sir Jonathan was knighted in the Queen’s Birthday Honours list in 2017 for services to UK relations with the European Union.