It is a sequel to 1944 film Going My Way, with Crosby reprising his role of Father Chuck O'Malley, all-around cool Catholic priest. Father O'Malley has been sent to St. Mary's, a dilapidated, crumbling Catholic school, where he will serve as the pastor/principal, evaluating the school and reporting to his superiors whether or not it should be closed. Sister Mary Benedict (Bergman), the head nun at the school, very much wants to keep it open. She is leaning on Horace Bogardus, a businessman who has purchased the neighboring lot and is building a factory; Sister Benedict wants Bogardus to donate the neighboring building to the school. Other problems at St. Mary's include Eddie, a meek student and victim of bullying that Sister Mary mentors, and Patsy, a child of a broken home that St. Mary's has taken in as a boarding student.
- Boxing Lesson: Sister Benedict trains Eddie how to box in order to fight his bully. She goes so far as to get a how-to-box manual from a sporting goods store, before teaching Eddie how to move his feet and dodge punches and throw a right cross, etc.
- Broken Glass Penalty: The kids are playing baseball when one of them hits a ball through a window at Mr. Bogardus's factory. He turns to see Sister Benedict, who was trying to teach the girls how to hit, running for cover.
- Child Hater: Mr. Bogardus admits that he's never liked children, but he turns over a new leaf and hands his building over anyway as an act of charity.
- Cool Teacher: All in all, Sister Benedict is pretty cool. She teaches a kid how to box!
- Disappeared Dad: Patsy Gallagher's musician father left for a gig shortly after becoming married, and never returned, leaving Mrs. Gallagher to prostitute herself to support Patsy.
- Easily Forgiven: Mr. Gallagher left before Patsy was even born, leaving Mrs. Gallagher all alone, forcing her into prostitution. When he returns 13 years later, she welcomes him with open arms and they get back together immediately.
- Establishing Character Moment: Mr. Bogardus gets out of his car and immediately starts yelling about all the kids at St. Mary's who are playing in his half-built factory. He is established as cranky and irascible.
- Getting Crap Past the Radar: Without coming out and saying so, the film makes clear that Patsy Gallagher's mother has been supporting herself and her daughter by prostituting herself.Father O'Malley: You've been supporting her all this time?
Mrs. Gallagher: Mm-hmm. I suppose you're wondering as to how. So is she. She's getting to be a big girl now. She's beginning to think I'm no good. I want to put her in your care...before she finds out she's right.
- Held Back in School: A point of argument between Sister Benedict and Father O'Malley. Patsy has failed her exams, and on that basis, Sister Benedict wants to hold her back. Father O'Malley wants to pass her, on the grounds that St. Mary's should be in the business of helping its students. Subverted when Patsy eventually reveals that she failed her exams on purpose in order to stay longer at St. Mary's.
- Hollywood Nuns: The nuns at St. Mary's are straight out of central casting, with the full penguin suit and everything.
- Locked Out of the Loop: Causes a bit of Conflict Ball late in the film, when a doctor diagnoses Sister Benedict with early-stage tuberculosis, decides that she should go to someplace dry like Arizona to recover—and prevails upon Father O'Malley not to tell her why she's getting transferred. Father O'Malley caves just as Sister Benedict is leaving and tells her why. She is relieved.
- Mars-and-Venus Gender Contrast: Aspects of this in the relationship between Father O'Malley and Sister Benedict. Father O'Malley worries that being raised by a bunch of nuns will turn the boys of the school into sisses, while Sister Benedict is skeptical of the virtues of male aggression.
- The Matchmaker: Father O'Malley finds Mrs. Gallagher's long-lost husband and brings him back so they can get back together.
- Nuns Are Funny: There's a little bit of Cloud Cuckoolander running through the nuns of St. Mary's. Father O'Malley is visibly startled when an alarming number of nuns enter the meeting room on the day of his arrival. Then he is thrown off his game when the nuns start laughing and giggling through his speech—they're laughing at a cat behind him that has gotten into his hat.
- Plagiarism in Fiction: After Father O'Malley gives Patsy a talk on her assignment—write about the five senses—Patsy shamelessly steals everything he said for her presentation to the class, and steals some other stuff as well.
- Protagonist-Centered Morality: Father O'Malley and the nuns of St. Mary's pressure Mr. Bogardus into turning over his factory to them; they are not troubled by the 300 jobs that will not be created. It gets even worse when Father O'Malley conspires with Mr. Bogardus's doctor to push him into handing over the building because it will supposedly help his heart.
- Single Mom Stripper: Mrs. Gallagher has been hooking to support herself and Patsy.
- Teach Him Anger: Sister Benedict has to teach meek little Eddie how to be more aggressive so he can stand up to his bully.
- Tomboy: Dialogue reveals that Sister Benedict used to play baseball and football with the boys when she was a kid. She teaches Eddie how to box and teaches a girl student how to swing a baseball bat.
- Turn the Other Cheek: Eddie does this with his bully, proudly reciting the lessons that Sister Benedict taught him. Since this resulted in Eddie taking a beating, Sister Benedict changes her mind and decides to teach him how to fight.