Social Bite, which has cafes in Edinburgh, Glasgow and Aberdeen, employs and supports homeless people and 100 percent of its profits go to charity.
The new funding is the biggest single donation the chain has received since being set up by Josh Littlejohn and Alice Thompson in 2012.
Social Bite was in the spotlight last November when Hollywood star George Clooney paid a visit to the Rose Street branch to launch an appeal to help the homeless and fund an aid convoy to refugee camps across Europe.
In June, the Duchess of Cornwall visited the shop, and staff are also expected to welcome Oscar-winner Leonardo DiCaprio later this year.
The Big Lottery Fund cash will go towards running the Social Bite Academy, which has been set up to support the business model of employing a quarter of its staff from homeless backgrounds, as well as on extending opening hours to feed more homeless people.