The company will begin using heat-treated flour to enhance the safety of the product, spokeswoman Laurie MacDonald told USA Today Friday.
To make the switch, production of chocolate chip, oatmeal raisin, sugar and specialty doughs have been suspended at Nestle's Danville, Va., plant, where most of its refrigerated cookie dough is made.
MacDonald said two samples of cookie dough from the Danville plant recently tested positive for E. coli, which can cause severe illness. All of the dough was destroyed before it could be shipped, she said.
Dough production is to resume the week of Jan. 25, with tubes of the new cookie dough appearing on store shelves in early March.
The switch in production comes eight months after 72 people in 30 states were infected with E. coli after reportedly eating Nestle cookie dough raw.
'How to Train Your Dragon 2' releases 5-minute clip
Yosemite climber falls 30 feet, suffers major injuries