The company said 53 stores will lose plastic bags at checkouts from Monday, with all 2,485 sites only offering customers paper bags from early next year.
However, Boots will continue to charge customers for the new unbleached brown bags, despite them not falling under the plastic bag tax.
Managing director Seb James said the decision means 900 tonnes of plastic will be removed from his stores as a result.
He added: "Plastic waste is undoubtedly one of the most important issues around the world today, with TV shows like Blue Planet highlighting the effects of plastic pollution.
• READ MORE: Chefs ditch avocados from Scottish menus in bid to be more environmentally friendly"This year, we are transforming Boots as we celebrate 170 years, and the move to unbleached paper bags is another pivotal moment in that journey. There is no doubt that our customers expect us to act and this change signifies a huge step away from our reliance on plastic."
Hundreds of companies have already made pledges to cut back the amount of plastic and packaging they use.
Earlier this month, Waitrose unveiled a new "plastic-free" store, McDonald's is replacing plastic straws with paper ones, and supermarket Iceland has promised to end plastic packaging from own-label products by 2023.
• READ MORE: Sainsbury's first supermarket to axe plastic bags in all storesHelen Normoyle, director of marketing at Boots, said: "Our new paper bags have been carefully tested to make sure that, over their entire lifecycle, they are better for the environment, whilst still being a sturdy, practical option for customers who haven't brought their own bags with them when shopping."
The recycled brown bags cost 5p, 7p and 10p, depending on size, and the company said all profits will be donated to BBC Children in Need.
Scottish Store list:
Edinburgh 101 Princes Street
Aberdeen Bon Accord Centre
Glasgow Braehead Centre
Glasgow Buchanan Gallery