The app's new capability is only available to users who load their prepaid account before entering a location. The app then communicates with the cash register to confirm the order.
Harris+Hoole said all of its 36 outlets would be able to accept payments via the app by 1 July.
Danielle Anderson, director of digital experience for Harris+Hoole, said: "The mobile payment removes the cold formality of an anonymous transaction and better reflects the kind of friendly exchange you'd expect from your local coffee shop.
"For the first time anywhere in the UK, a customer can walk into any H+H shop, order their usual from a barista who knows their name and how they like their coffee, and pay, all from just one tap on their mobile."