[6] In 1910, William Bateson became the first director of the John Innes Horticultural Institution and moved with his family to Merton Park.

John Innes compost was developed by the institution in the 1930s, who donated the recipe to the "Dig for Victory" war effort.

The John Innes Centre has a contingent of postdoctoral researchers, many of whom are recruited onto the institute's Post-doctoral Training Fellowship programme.

[12] In February 2025, the John Innes Centre announced the appointment[13] of Professor Cristóbal Uauy as its next director, effective September 2025.

[14] These ISPs, which combine the research of multiple groups to address a greater aim, were, from 2017 to 2023 as follows: The John Innes Centre co-located with The Sainsbury Laboratory (Norwich),[15] an institute focused studying plant disease.

Currently, the JIF owns the land and buildings at Newfound Farm in Bawburgh, Norfolk which are used by researchers from the John Innes Centre.

The JIF trustees also play an active part in the management of John Innes Centre research and have the right to appoint three members of the Governing Council.