It is the latest restructuring by the John Lewis Partnership.
The company said the shake-up will take place as part of a simplification of store management.
It comes after a raft of recent job cuts, which included the closure of eight John Lewis stores earlier this year.
The company currently operates 331 Waitrose stores and 34 John Lewis shops across the UK.
JLP added that it will support employees who wish to stay in the business in finding new roles and will seek to minimise compulsory redundancies through voluntary redundancy and severance options.
A John Lewis Partnership spokesperson said: “We have announced to our partners our intention to simplify our management structures in Waitrose and John Lewis stores, which will allow us to reinvest in what matters most to our customers.”