The changeover starts today, 53 stores will no longer offer plastic bags at checkouts.
All 2,485 sites will only offer customers paper bags from early next year, according to the company.
It is hoped that the decision means 900 tonnes of plastic will be removed from store operations as a result.
Boots will charge customers for the new unbleached brown bags, despite them not falling under the plastic bag tax. 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.
Managing director Seb James said: "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.
"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.
Helen 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."