Dame Sharon White, chairman of the retail group, told staff on Thursday the announcement "will come as a blow".
The group posted a £55m loss for the six months to July 25 after higher costs offset a rise in revenues.
The Peterborough store, located in the Queensgate Centre, was one of the last to re-open after the Covid lockdown, with many worrying that it could be one of the stores set to close for good. However, it reopened on July 30 with queues of people waiting to get back in, but staff have taken to Facebook to share that footfall has been down.
John Lewis says that online orders now account for 60% of total sales - up from 40% before the pandemic hit.
Dame Sharon White explained: "The pandemic has brought forward changes in consumer shopping habits which might have taken five years into five months.
"Both brands (Waitrose and John Lewis) entered the crisis with strong and established online businesses and in the case of Waitrose, plans for expansion are well under way in preparation for the end of the relationship with Ocado. Our digital businesses have been key to underpinning our first half performance."
This week the partnership announced they would be closing four Waitrose sites as they look to turn restructre. Stores in Ipswich, Caldicot and Shrewsbury will close while the Wolverhampton branch will be sold to Tesco.