Professor Dale Sanders is a leading light on chemicals in plant cell membranes and used to head the department of biology at the University of York.
Sanders specialises in crop traits such as nutritional values, seed germination, the response to drought conditions and how plants cope with toxic compounds in the soil.
He works on the poorly-understood role of chemical transport mechanisms in plants and has written more than 140 scientific papers.
"The John Innes Centre has an unrivalled global reputation for excellence in plant and microbial sciences," said Sanders.
"Its scientists can help to shape the world by contributing to developing new, higher-quality or disease-resistant crops to improve food security."
The Biotechnology & Biological Sciences Research Council (BBSRC), John Innes Foundation and the John Innes Centre Governing Council made the appointment together.
BBSRC chief executive Professor Douglas Kell said Sanders was a leading and internationally-recognised scientist with a record in plant membrane transport.
"He will build on the strong legacy of the previous director, the late Chris Lamb, and contribute to our aim of strengthening global food security and industrial biotech," said Kell
Sanders gained a PhD at the University of Cambridge, has held a fellowship at Yale School of Medicine and was elected a fellow of the Royal Society in 2001.
The John Innes Centre is one of the world's leading centres of excellence in plant and microbial science, founded as the John Innes Horticultural Institution in 1910.