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.
Eight John Lewis stores – including its Aberdeen branch – have closed this year.
The company currently operates 331 Waitrose stores and 34 John Lewis shops across the UK.
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There are currently only two John Lewis stores – one in Edinburgh and one in Glasgow – across Scotland.
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."