The issue meant shops were unable to accept payments.
Technical problems which forced Greggs stores across the UK to close on Wednesday morning have been resolved, the bakery chain said.
The IT outages prevented payments from being accepted and the issue affected branches nationwide, including in London, Sheffield and Birmingham.
Some stores put up temporary “closed” notices on their doors, others were only able to accept cash payments, and some told customers to order outside on the Greggs mobile app before their food could be given to them.
Later in the morning, Greggs said the “majority of shops affected are now able to take card and cash payments again” and it soon expects the issue to be fully resolved.
A Greggs spokesperson said: “We have now resolved the technical issue that affected tills in some of our shops earlier this morning.
“We apologise for the inconvenience this may have caused to our customers.”
Greggs operates more than 2,450 shops across the UK, though it is unclear how many were affected by the technical problems.
The popular bakery chain was the most recent of several retailers to suffer problems with their payments systems.
On Saturday, Sainsbury’s and Tesco stores across the UK were unable to accept contactless card payments and could not issue some home delivery orders.
McDonald’s suffered a “global technology system outage” on Friday, which the fast-food chain said had not been “directly caused by a cybersecurity event”.
