The shops in Sheffield and at the Vangarde Shopping Park in York are two of eight stores proposed for permanent closure.
John Lewis said it will enter into consultation with the 209 staff affected in York and 299 in Sheffield. The retailer added that it will look to find alternative roles in the partnership for as many staff as possible.
Sharon White, chairwoman of the John Lewis Partnership, said: “We appreciate this is incredibly difficult news for our Partners and the people of Sheffield.
"We are acutely aware of our long history in the city and are hugely grateful to all our customers in Sheffield for their loyalty, our partners for their outstanding work over the years and Sheffield City Council for its continued support.
"While the shop was financially challenged prior to the pandemic, we were determined that with additional investment, we would be able to play a key role in the regeneration of the city centre.
“However, the pandemic has had an irreversible impact on retail and we must make difficult decisions to ensure the Partnership is sustainable in the future.
“If the proposal to close goes ahead, we have put together a package of carefully considered support to help our partners and would look to redeploy as many partners as possible.”
Patrick Duffy, head of branch for John Lewis Sheffield, said: “John Lewis holds a special place in my and many people’s hearts in Sheffield, as we have had a presence in the city since 1940.
"We are incredibly proud of the long and valued legacy of service we’ve held in Sheffield and thank our customers for shopping with us over many years.
"I also want to thank our partners for all their hard work as we continue to support them through the consultation period.”
Kylie Gilson, head of branch for John Lewis York, said: “It has been a huge privilege to work alongside such brilliant Partners at the Vangarde Shopping Park and it is with a heavy heart that we share the proposal to close the store.
"We hope that if the closure goes ahead we would still see many of our customers in nearby Waitrose shops and John Lewis Leeds.”
Dan Jarvis, mayor of Sheffield City Region, said losing John Lewis in the city was "another blow to retail workers who are among those who have been hit hardest by the pandemic".
He added: “The store has been a cornerstone of the city’s retail offer for more than a century. I am working with John Lewis and Sheffield City Council to determine what this means for those whose jobs are now on the line and what can be done to support them.
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