The UK baker, also known for its steak bakes, vegan snacks and sweet treats, closed all of its more than 2,050 shops on March 24 when the country went on coronavirus lockdown.
Thursday's reopening for takeaway only, and with a menu limited to best sellers, follows a successful trial of a small number of shops which tested operational changes, including new workwear, equipment and social distancing measures.
Greggs plans to open the rest of its shops in early July.
The group said it could not predict the impact of social distancing on its ability to trade or on customer demand.
"However, our capacity to operate will be restricted by size of shop and we must anticipate that sales may be lower than normal for some time," it cautioned.
It said it would keep a proportion of its 25,000 staff on the government's job retention furlough scheme until sales levels begin returning to normal.