In New York City, mortgage broker Ted Haines, Sr. reluctantly tells elderly Irish priest Father Fitzgibbon that if the overdue payment on St. Dominic's church is not soon received, he will call in the mortgage. Haines's son Ted, Jr. urges leniency, but his father is adamant. Father Charles Francis Patrick O'Malley arrives in St. Dominic's neighborhood and makes a bad impression on a few neighbors because of his easy-going and unconventional manner. By the time Father O'Malley introduces himself to Father Fitzgibbon as his new curate, he has donned a sweatshirt and casual pants, and immediately puts the very traditional Fitzgibbon on his guard. The next day, O'Malley is visited by his childhood friend, Father Timothy O'Dowd, a jocular priest from the neighboring parish. Only O'Dowd is aware that O'Malley has been sent to take over the pastorship of St. Dominic's, which, in addition to being in financial trouble, is in a troubled neighborhood. When Ted, Jr. tries to evict Hattie Quimp, who initially found O'Malley to be a nuisance, O'Malley intercedes and promises that the church will guarantee her rent. As he is walking back to St. Dominic's, O'Malley sees teenagers Tony Scaponi and Herman Langerhanke stealing turkeys from a truck. The boys escape into the church garden where they encounter Fitzgibbon, to whom they give one of their stolen turkeys as a gift. That night over their turkey dinner, O'Malley suggests that the boys are delinquents, and Fitzgibbon defends the boys until he learns of their theft. Instead of punishing the boys, however, O'Malley takes them to a baseball game. One day, Officer Patrick McCarthy brings eighteen-year-old runaway Carol James to see O'Malley. O'Malley, who had had his own band and composed music before entering the priesthood, coaches Carol on her singing, but when she rejects his offer of a housekeeping job at the church, he urges her to return home. Knowing she will not take his advice, O'Malley loans Carol ten dollars. After earning the trust of the boys's gang, O'Malley convinces them to train as a choir. When sounds of the boys rehearsing "Three Blind Mice" rise into the church from the cellar, Fitzgibbon loses his patience with O'Malley's unconventional methods and goes to see the bishop to ask for O'Malley's transfer. Fitzgibbon returns deflated, as he has learned that the bishop sent O'Malley there to take over for him. Distraught by his apparent retirement, Fitzgibbon runs away, but O'Malley puts McCarthy on the alert, and he returns late that evening with a storm-bedraggled Fitzgibbon, who is then coddled by O'Malley and the housekeeper, Mrs. Carmody. The two priests share a sip of whiskey, and Fitzgibbon confides his longing to see his ninety-year-old mother, who still lives in Ireland, after which O'Malley soothes him with an Irish lullaby. Not long after, O'Malley encounters another childhood friend, Metropolitan Opera star Genevieve Linden, who is surprised that her old flame "Chuck" has become a priest. When Mrs. Quimp informs Fitzgibbon that Carol has taken an apartment across from hers and is receiving visits from Ted, Jr., O'Malley is sent to "handle" the situation. O'Malley learns that Ted, Jr. and Carol met on the street and fell in love immediately, and that Ted, Jr. has let her live in a vacant apartment without his father's knowledge. Some time later, Jenny and O'Dowd visit St. Dominic's and make an appreciative audience when O'Malley rehearses the boys choir. O'Dowd reports that he has shopped around for publishers for O'Malley's original song, "Going My Way," but that publishers rejected the "schmaltzy" song. When Ted, Sr. comes to the apartment to discover why his son quit his job and has disappeared for two weeks, he discovers that Ted and Carol have married. The newlyweds are blissfully happy despite Ted, Sr.'s ire, but his anger soon dissipates when Ted, Jr. dons an Army Air Force uniform, and, after bidding Carol a loving farewell, reports for service. O'Dowd, meanwhile, lures his friend, Max David, a music publisher, and Max's partners, to the Metropolitan Opera House, where Jenny has arranged for the orchestra and St. Dominic's boys choir to back her as she sings a classical arrangement of "Going My Way." The publishers gently reject the song as too highbrow, but are delighted by O'Malley's more upbeat song, "Swinging on a Star." Instead of paying O'Malley directly for the song, Max and his partners surreptitiously deposit a huge payment in the collection box during Fitzgibbon's Sunday sermon at O'Malley's suggestion. Fitzgibbon is elated by the generous donations of his parishioners, which is enough to make the mortgage payments, and he even accompanies O'Malley and O'Dowd when they play golf. Fitzgibbon's happiness comes to an abrupt end, however, when the church burns down. The elderly priest loses all hope and falls ill after he collects only thirty-five dollars from a neighborhood collection. O'Malley then tells Fitzgibbon that Ted, Jr. has had a minor jeep accident and will be returning home, and really lifts the pastor's spirits when he tells him that Jenny, who has taken the boys choir with her on a concert tour, has sent a $3,500 check from the proceeds. Construction soon begins on the new church, and O'Malley informs Fitzgibbon that he has been transferred to another church for the same type of assignment. Fitzgibbon, now fond of O'Malley, is sad to see him go and is chagrined when O'Dowd becomes his new curate. As Fitzgibbon praises O'Malley to his parishioners and informs them of his departure, Jenny brings in Fitzgibbon's elderly mother by arrangement with O'Malley. Fitzgibbon tearfully embraces his mother for the first time in forty-five years, and O'Malley walks away into the night.