The “evolving pop-up” opened as a sit-in dining space to serve the adjacent St John Bakery in Maltby Street Market in 2014, but it will close its doors on 24 June.
A spokesperson says the group was always “restricted” in its ability to meet customer demand due to the constraints of the building, facilities and license, so is focusing on a new area of growth.
St John is aiming to launch two permanent bakeries in central London this summer, with the sites currently “under negotiation”.
It says there is “significant demand” for the openings shown by the success of its two bakery pop-ups in Old Street Station and Bermondsey Street.
The original St John Bakery opened on London’s Druid Street in 2011 and sells sourdough, doughnuts and more to restaurants, cafes and retail sites across London.
It is part of the wider St John group, which includes three restaurants, the bakery and a winery.
The first St John restaurant was opened by Fergus Henderson and Trevor Gulliver in 1994, offering a nose-to-tail cooking approach that helped define modern British cuisine. It has maintained a Michelin star since 2009.
Malty Street’s head chef Alex Szrok and manager Rebecca McGauley-Dyke will continue to work at the company at St John’s Smithfield going forward.