The chef opened the 120-cover grill and deli as part of his consultancy with Restaurant Associates, the fine dining arm of catering firm Compass Group, in 2016.
It sat next door to Atherton’s City Social restaurant in Tower 42 in the City, which is also run with Compass.
In a joint statement, Atherton and Restaurant Associates said: “In order to focus on other areas of our ongoing partnership, we have taken the decision to close Temple and Sons.
“We are firm believers in chef and restaurant partnerships, championing exciting opportunities and we’re looking forward to our continued work at Michelin-starred City Social and throughout other areas of the Restaurant Associates business.”
Atherton has been a consultant chef for Compass since 2010 and renewed the partnership for five years in 2015.
Last month his Japanese restaurant Sosharu closed its doors after struggling with its Farringdon location. It is rumoured to be relocating to a more central site in Soho or Mayfair.
Atherton's Social Company group runs 15 restaurants worldwide in cities including London, New York, and Dubai.