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Bowen was elected a Fellow of the Royal Society for the encouragement of Arts, Manufactures and Commerce (RSA) in 2002 and of the British Computer Society (BCS) in 2004. He is a Liveryman of the Worshipful Company of Information Technologists in the City of London.

Bowen's other major interest is the area of online museums. In 1994, he founded the Virtual Library museums pages (VLmp), an online museums directory that was soon adopted by the International Council of Museums (ICOM). In the same year he also started the Virtual Museum of Computing. In 2002, he founded Museophile Limited to help museums, especially online, for example with discussion forums. He has also worked in industry at Oxford Instruments, Marconi Instruments, Logica, Silicon Graphics, and Altran Praxis.

Bowen later worked at Imperial College, London, the Oxford University Computing Laboratory (now the Oxford University Department of Computer Science), the University of Reading, and London South Bank University. His early work was on formal methods in general, and later the Z notation in particular. He was Chair of the Z User Group from the early 1990s until 2011. In 2002, Bowen was elected Chair of the British Computer Society FACS Specialist Group on Formal Aspects of Computing Science. Since 2005, Bowen has been an Associate Editor-in-Chief of the journal Innovations in Systems and Software Engineering. He is also an associate editor on the editorial board for the ACM Computing Surveys journal, covering software engineering and formal methods. From 2008–9, he was an Associate at Praxis High Integrity Systems, working on a large industrial project using the Z notation.

Jonathan P. Bowen FBCS FRSA (born 1956) is a British computer scientist.