The four-time Tony Award nominee is expected to take over the role of Sister Aloysius in the Tony Award- and Pulitzer Prize-winning play, as of Jan. 10.
Cherry Jones is expected to play her final performance as the tough-as-nails Bronx nun Jan. 8.
Negotiations are ongoing with a male star to play opposite Atkins and additional casting will be announced shortly, producers for the show said in a statement.
Atkins' Broadway credits include "The Killing of Sister George," "The Promise," "Vivat! Vivat! Regina," "Indiscretions (Les Parents Terribles)" and "The Retreat from Moscow."
Her film credits include "Cold Mountain," "Vanity Fair," "Ask the Dust," "The Queen of Sheba's Pearls," "The Hours" and "Gosford Park."
Set in a Catholic school in 1964, "Doubt" is the story of a nun faced with the difficult decision of whether to voice concerns about one of her male colleagues even though she is uncertain of the truth of her allegations.