Owned by investment group JAB Holdings, Pret permanently closed 30 UK shops and cut 2,800 jobs, or a third of its workforce in August.
The firm said that over the last four months it had seen consistent sales growth, with consecutive weeks of trading progress since April. However growth has slowed since the end of September.
On Sept. 22 Prime Minister Boris Johnson told Britons to work from home where possible as infection rates increased.
Pret has 389 shops in the United Kingdom, with many located on high streets, at transport hubs and close to offices that are still largely deserted.
"The worsening rates of COVID-19 and the impact on trade in the City of London have meant Pret's recovery has suffered a setback," said Pret's UK managing director Clare Clough.
"The changes Pret is announcing today will enable Pret to continue to adapt through the winter."
To help it survive the crisis, Pret last month launched a subscription service for drinks.
It is also selling coffee beans through Amazon and has new partnerships with Deliveroo, Just Eat and Uber Eats.
Pret employs about 9,000 globally, including 6,500 in the UK.
(Reporting by James Davey, editing by Louise Heavens)