The Soil Association says its award recognises restaurants and caterers who serve local, fresh and honest food, which is free from controversial additives and better for animal welfare, and includes a rigorous on-site inspection.
The catering team serves up to 2,500 people a day at the high-end department stores Victoria HQ.
The team's head chef, Dan Blackburn, said: "It is such a big achievement for us and an amazing step in the right direction for workplace nutrition.
“As head chef, my food ethos is about ensuring we deliver quality food at prices that are accessible for everyone. I strive to use fresh ingredients wherever possible...the more we can encourage our partners to eat healthily, responsibly, and seasonally, the better.”
Options available at the restaurant includes sourdough pizzas served from a new pizza oven, a salad bar and a nutritional counter serving healthier options.
John Lewis joins Jaguar Landrover, Selfridges staff restaurants, Scottish parliament and City Hall London as winners of the award.
The Soil Association's Lizzi Testani said: "It is fantastic that the catering team at the head quarters at John Lewis are not only serving tasty meals to partners but have also used the award to ensure that those meals are sustainably sourced and highlight provenance."