In 1964 at a Catholic church in The Bronx, New York, Father Brendan Flynn gives a sermon on the nature of doubt, noting that it, like faith, can be a unifying force. Sister Aloysius, the strict principal of the church’s parish school, becomes concerned when she sees a boy pull away from Flynn in the school courtyard. She instructs her Sisters to be alert to suspicious activity in the school.
Sister James, a young and naive teacher, receives a request for Donald Miller, an altar boy and the school’s only African-American student, to meet Flynn in the rectory. Donald returns to class visibly upset, and James notices the smell of alcohol on his breath. Later, she sees Flynn placing an undershirt in Donald’s locker. She reports her suspicions to Aloysius.
Aloysius and James confront Flynn. Flynn denies wrongdoing, claiming Donald had been caught drinking communion wine and that he called him to dismiss him as an altar boy. James is relieved by Flynn’s explanation, but Aloysius is not convinced. Flynn delivers his next sermon on bearing false witness and gossip. James later asks Flynn about the shirt he put in Donald’s locker, an observation she kept from Aloysius. Flynn explains that Donald had left the shirt in the sacristy, and that he put it in his locker to spare him additional embarrassment.
Aloysius meets with Donald’s mother regarding her suspicions and is shocked by her seeming disinterest in Flynn’s alleged abuse. Mrs. Miller admits that she would turn a blind eye to the abuse, if it existed, in order to keep Donald in a school that will better his socioeconomic situation and to further protect him from his physically abusive father; Mrs. Miller confesses that she knows Donald is gay, and she fears that his father would kill him if he knew about what happened with Flynn.
Aloysius confronts Flynn and demands his resignation. She claims to have contacted a nun from one of his previous parishes who corroborated her suspicions, and threatens to visit his previous appointments and contact parents. Flynn agrees to request a transfer and delivers a final sermon before departing.
Some time later, Aloysius tells James that Flynn has been appointed to a more prestigious position at a larger church. She admits to having lied about contacting a nun at Flynn’s former church, but believes his resignation is proof of his guilt. She then breaks down in tears, saying to James, “I have doubts…I have such doubts.”