The company said the shake-up will take place as part of a simplification of store management.
It told staff that the move will allow it to reinvest to improve the experience of customers, with investment in frontline customer service and visual marketing.
The move comes just four months after the retailer confirmed the closure of eight more stores, impacting upon 1,465 jobs.
It also comes around a year after a previous shake-up, which had cut another eight stores and 1,300 jobs, in the first stage of its sweeping overhaul.
JLP has pushed forward with the raft of cuts in a bid to meet its target of £300 million in savings by 2022.
Earlier this month, the partnership announced plans to build 10,000 rental homes over the next few years in a bid to return to profit by diversifying its operations.
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.
The company said the changes will reduce the number of layers between its most senior leaders and non-management shop-floor staff.
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.”
Earlier this year, the retailer also said it expects its financials to get worse over the current financial year as it continues its shake-up and warned staff they are not expected to receive a bonus until 2022-23.