The high-street chain, which has 2,700 UK locations, says it has launched a consultation process with staff to try and relocate team members facing redundancy.
It suggests the role of assistant store manager will be axed across its UK business.
So far 2,400 Costa sites have reopened, and while the Coco-Cola owned business says trade is returning, buoyed by the Government's Eat Out To Help Out scheme in August, there remains 'high levels of uncertainty' as to when it will return to pre-Coronavirus levels.
"Today's announcement to our store teams was an extremely difficult decision to make," says Neil Lake, managing director for Costa Coffee UK and Ireland.
"Our baristas are the heart of the Costa business and I am truly sorry that many now face uncertainty following today's news.
"We have had to make these difficult decisions to protect the business and ensure we safeguard as many jobs as possible for our 16,000 team members, while emerging stronger ready for future growth.
"As a proud member of the UK high street, we remain committed to the role Costa plays in supporting the economic recovery of the country, but today I want to say a huge thank you to all of our team members that are affected by this announcement and we will be supporting you throughout this process."
Costa’s announcement comes less than a week after similar news from Pret, which is to cut nearly 2,900 jobs and close 30 stores.