It is Christmas Eve in 1977 at a disco nightclub in Philadelphia. Club singer, Deloris Van Cartier, and her two back-ups are performing in front of an empty house. A gangster and four henchmen appear. Van Cartier's boyfriend, Curtis Jackson, owns the nightclub ("Take Me to Heaven"). Deloris is overjoyed as she believes her boyfriend is going to introduce her to a record producer on that day. She soon learns, however, that this is not to be. Jackson tells her he cannot join her for Christmas Day but gives her a coat, which she discovers belonged to his wife. Hurt and frustrated, Deloris goes to her backup singers, Michelle and Tina, about her dreams of stardom and fame ("Fabulous, Baby!") She decides to break up with Jackson and head out of Philadelphia to go fulfill her dreams on her own. When she happens to witness Jackson and his crew murder someone accused of "squealing" to the cops, though, she becomes terrified. Deloris promptly runs away as Jackson orders his men to get her and bring her back.
Some time later, Deloris runs into a police station and tells the desk chief, Eddie, about what has happened. The two recognize each other as old friends from school, with Deloris calling him "Sweaty Eddie." Eddie decides that Deloris needs to go into the witness protection program and sends her to the place he believes Jackson will never find her: a convent! When Deloris arrives, she is disappointed to learn from the Mother Superior that contact with the outside world is limited and that she cannot smoke, drink or wear any of her less-than-appropriate clothing ("Here within These Walls").
Deloris joins the other nuns for dinner and is introduced as Sister Mary Clarence. After several comedic interactions with the overly perky Sister Mary Patrick, Deloris discovers just how much is limited when she is a nun ("It's Good to Be a Nun"). Deloris then asks them about what they're missing, and Mother Superior makes Deloris go on a fast. Meanwhile, back in his nightclub, Jackson is frustrated that he cannot find Deloris anywhere. He tells Joey, TJ and Pablo how he will not stop until he finds and kills Deloris ("When I Find My Baby").
Back at the convent, Deloris is hungry from the fast. She goes across the street to a slinky bar and is followed by Sister Mary Patrick and Sister Mary Robert, a shy and quiet nun. When the two nuns arrive, they see how fun things can be outside of the convent. However, Deloris recognizes Joey, TJ and Pablo entering the bar. Suddenly, there is a fight in the bar, giving Deloris, Sister Mary Patrick and Sister Mary Robert a chance to escape. Eddie and Mother Superior meet them back at the convent. Mother Superior confronts Deloris, telling her that she must conform to the life of the nuns. Eddie agrees and reveals that Jackson has upped the price on her head, so she needs to be careful. Deloris storms back to the convent after being informed that she has to wake up at 5 a.m. and join the choir. Eddie, now alone with only the drunks and homeless on the street, privately reflects on his desire to just let go and impress Deloris ("I Could Be That Guy").
The following morning, Deloris attends the choir practice and realizes how bad the situation is. Deloris offers to teach them, thus taking over from Sister Mary Lazarus, an older nun. Deloris teaches the nuns how to sing in key and on time. She also manages to break the quiet and timid Sister Mary Robert out of her shell ("Raise Your Voice"). That Sunday, the choir performs a rousing, up-tempo hymn ("Take Me to Heaven – Reprise"). Although the church is struggling, the improved performance and new material bring an influx of donations and membership. Mother Superior, however, is horrified at how the simple, traditional choir she knew has changed and become modern.
Mother Superior wants to get rid of Deloris, but Monsignor O'Hara reminds her that the men who were planning to buy the church love the choir and have given their money to improve and keep the church... specifically because of the choir. Over the last few weeks, the choir has become incredibly successful, and the money from donations has paid for the church to be remodeled and fixed ("Sunday Morning Fever").
Later, Monsignor O'Hara bursts in with exciting news: the choir has been asked to perform a special concert in front of the Pope. Deloris is thrilled but also regretful; Jackson and his goons have spotted Deloris with the choir on the television accepting the invitation. Jackson orders his henchmen to get into the convent and bring Deloris back. TJ, Joey and Pablo discuss how they will do this ("Lady in the Long Black Dress"). Meanwhile, Mother Superior prays to God, asking why He has given her the challenge that is named Deloris ("I Haven't Got a Prayer"). She soon receives a call from Eddie.
Deloris is approached by the Nuns before they go to sleep, asking her to lead them in prayer for their show for the Pope on the following day ("Bless the Show"). Mother Superior arrives shortly thereafter and informs Deloris that the court date for Jackson has been moved up to the next day and she must leave immediately. The other nuns overhear, and Deloris is forced to tell them the truth about who she really is and that she cannot perform with them. Deloris quickly runs off to get her things, followed by Sister Mary Robert while the other nuns disappointingly go back to their rooms.
As Deloris prepares to leave, Sister Mary Robert begs to come with her, claiming that she has been inspired to become a stronger person and go after the things she wants ("The Life I Never Led"). Deloris tells her that she doesn't need her to do that and that she can do it all herself if she really wants to. Deloris runs from the convent and stays at Eddie's house for the night. While there, she is initially overjoyed that, the following day, she will testify against Jackson and his boys to go back to pursuing the career she's dreamed of ("Fabulous, Baby! – Reprise"). But feeling immense guilt for abandoning her sisters when they needed her, she begins to reflect on her life, finally realizing that the choices she is making will leave her with nothing but fame and money. She decides to return to the convent and sing with her sisters ("Sister Act").
Elsewhere, Jackson thinks up a new way to get into the convent ("When I Find My Baby – Reprise"). Dressed as nuns, Jackson, Joey, TJ and Pablo sneak into the convent. They find and chase Deloris. The Nuns see this and they all prepare to protect Deloris. Mother Superior, however, is adamant that they stay away and call the police, which prompts an outburst from Sister Mary Robert, who tells her that she won't be quiet anymore ("The Life I Never Led – Reprise"). The other nuns agree and all go running through the convent to look for Deloris.
Deloris eventually runs into Jackson, leading to a final confrontation. He is armed and dangerous, and she is scared but calm. Jackson demands that Deloris to get on her knees and beg for her life. However, all the sisters and nuns run in, unafraid; they stand in front of her, telling Jackson that they will have to go through them first ("Sister Act – Reprise"). Jackson is about to start firing at the nuns when Eddie comes in and fights Jackson off. He arrests Jackson and his boys. He and Deloris then share a passionate embrace. Mother Superior and Deloris come to a truce and agree to accept each other – warts and all. As the curtain begins to fall, we transition to the performance in front of the Pope as the nuns stand in unison with their voices ringing in harmony, led by a changed Deloris Van Cartier ("Spread the Love Around").