The company said 53 stores will lose plastic bags at checkouts from Monday, with a further 2,432 shops only offering customers paper bags from early next year.
Boots will continue to charge customers for the new brown bags, despite them not falling under the plastic bag tax. The bags will cost 5p, 7p and 10p, depending on size, and all profits will be donated to BBC Children in Need.
Some customers who have a repeat prescription will still get their medicine in plastic bags for now, but Boots says it is actively looking at alternative packaging options including cellulose, potato starch and a paper solution.
The retailer is the latest in a line of retailers that have taken pledges to cut back the amount of plastic and packaging they use. Earlier this month Waitrose unveiled a new “plastic-free” store, while supermarket Iceland has promised to end plastic packaging from own-label products by 2023.