The bonus, which is given out to all staff of the John Lewis Partnership under its employee-owned model, was six per cent last year, down from 10 per cent the year before.
The fall came as the retailer admitted pre-tax profits had fallen 77 per cent to £103.9m in the year to the end of January. Revenues edged up 1.8 per cent to £10.2bn, while sales rose two per cent to £11.6bn.
At Waitrose, operating profit before the partnership bonus fell 42 per cent to £119.8m, although it edged up 0.6 per cent to £232.9 at its John Lewis departments stores.
Sir Charlie Mayfield, the company's chairman, said 2017 had been a "challenging year".
"Consumer demand was subdued and we made significant changes to operations across the partnership which affected many partners."
He pointed to weakness in sterling putting pressure on cost prices, margins and leading to higher exceptional costs as it sped up changes to the business.
In October the company hiked pay to all for all its workers in non-management roles, pushing average pay for those who aren't managers to £8.91 per hour.
Yesterday the company came top of a ranking of UK retail employers, ahead of Lush Cosmetics, Ikea, Marks and Spencer and Clarks.