Inside, Butterfly sings "Vieni, amor mio!" ("Come, my love!") as she pulls special objects out of her sleeves. These objects include handkerchiefs, a pipe, a brooch, a mirror, a sash, and some various ornaments. When Pinkerton asks about a case she has brought, she tells him she cannot open it, since they are being watched. She tells him that it is her most sacred treasure. Goro tells Pinkerton that the case has a gift that the Mikado gave to her family, and that it is a sword for committing seppuku, or ritual suicide. This is how Butterfly's father died. Butterfly shows Pinkerton statues of her ancestors, and he mistakes them for dolls.
Butterfly then informs Pinkerton that she secretly went to the consulate and converted to Christianity. She did not consult with her uncle, a Buddhist priest, but did it in secret, to show her devotion to Pinkerton. She sings about the fact that it is her destiny to belong to the same church as Pinkerton.
Goro comes in and tells everyone to be quiet while the bride and groom sign the official papers. Pinkerton is announced as a lieutenant in the Navy stationed on the USS Lincoln. As the wedding celebration begins, the aria "Madama Butterfly" is sung and the wedding guests wish the couple well. Sharpless warns Pinkerton not to hurt Butterfly, then leaves, as the guests begin to toast and celebrate.
Suddenly, Butterfly's uncle, the bonze (monk), interrupts the celebration to sing "Cio-Cio San!" Cio-Cio San is Butterfly's name in Japanese, and her uncle warns her that she is damned. Having found out that she has left Buddhism behind, he warns her that there is now an ancestral curse on her.
As the bonze curses Butterfly, Pinkerton comes to her defense, but the bonze manages to get the other guests on his side. They renounce Butterfly, and leave, angrily. Left alone, Pinkerton tries to comfort the inconsolable Butterfly. He tells them that the people who have renounced her are not worth her tears.
The couple sings a love duet, "Bimba, Bimba, non piangere" ("Sweetheart, sweetheart, do not weep.") Pinkerton manages to comfort the weeping Butterfly, who feels like she can forget her family's curses and relish in her husband's comfort. Meanwhile, Suzuki says prayers in the next room. As night falls, the couple sings about the fact that Butterfly is all alone in the world. She suggests that, even though she is alone and disowned, she is happy. After closing up the house, Suzuki comes to help Butterfly get ready for her wedding night. They sing in separate rooms, Butterfly about the curse her uncle placed on her, and Pinkerton about his burning desire for her.
Butterfly is pleased to be with her husband, but is still upset about the fact that her family has cursed her. As Pinkerton sings about how beautiful she is, Butterfly compares herself to the moon goddess, "who at night crosses the bridge from heaven, steals hearts, wraps them in a white cloak, and takes them to her realm." Pinkerton begs her to tell him that she loves him, but she does not think she can bear it. She sings "Vogliatemi bene" ("Love me, please") and asks Pinkerton to show love to her, and proclaims his virtues. She also asks him about the foreign custom of pinning a butterfly's wings down. Pinkerton tells her that this does happen, but that it is actually done so that the butterfly does not fly away.
Pinkerton and Butterfly end their long duet with him continuing the butterfly metaphor and telling her that he has caught her so that he can hold her. She accepts this metaphor, as she believes that they are married for life, and feels some comfort. They sing about their desire for one another.
The contrast between Pinkerton's indifference to his marriage to Butterfly and her undying devotion is quite stark, and it only continues to become more and more evident as they embark on their marriage. Inside Pinkerton's house, Butterfly shows him her most treasured belongings, including a sword for seppuku. Then, she tells him that she has converted to Christianity for him. In a deeply-felt aria, she tells him that it is her destiny to go to church with him and leave her own traditions behind. While Pinkerton has made no real sacrifices or disclosed any real intimate truths about himself to Butterfly, she jumps into a marital relationship with him, and takes their bond quite seriously.
It seems that the community surrounding them is very supportive of the couple's union, until the ceremony is interrupted by the entrance of the bonze, Butterfly's uncle. He rails against his niece for leaving behind her religion and places a curse on her. Not only that, but he convinces the other guests at the wedding to join him in renouncing her. All of a sudden, Butterfly is not only getting cursed by her uncle, but also by the rest of her loved ones, who see her devotion to the American man as an immense betrayal. Quickly, Butterfly goes from "the happiest girl in the world" to a pariah in her own community.
With the renunciation of her family, Butterfly finds that her marriage to Pinkerton is even more important than it had seemed to her before. Now, not only does the union promise to relieve her from poverty, but it offers a home to her when her family has disowned her. She is horribly upset to be effectually kicked out of her family, but Pinkerton offers to take care of her in their stead. With nowhere else to turn, she falls easily into his arms, accepting the protection he offers in the face of her overwhelming loneliness. The fact that she needs the marriage now more than ever only intensifies the dramatic irony of Pinkerton's disloyalty to her, the fact that he plans to eventually leave her behind.
The metaphor of the butterfly only continues, as Pinkerton calls her his beautiful butterfly, and Butterfly worries about the implications of such a metaphor. When she suggests that it is customary in other countries for people to pin down the wings of a butterfly, worrying that this is a kind of brutality, Pinkerton insists that this is an act of care and desire, connected to the fact that the person who has the butterfly does not want to let it go. Rather than see this as a possessive and violent metaphor, Butterfly is blinded by her love and need for Pinkerton and accepts the image of a butterfly being kept in captivity as an image of care and affection.
The opera engages the themes of colonialism and American entitlement as well as love and sex. Pinkerton expresses his desire for Butterfly, even though he knows that he does not want to pursue a genuine relationship with her, thus taking on a colonial attitude towards their romance. He wants to lay claim to her and exploit her, without remaining loyal to her; this is, in effect, a colonial approach to his lover. Then, when she discusses her worries about the foreign custom of pinning down a butterfly, Butterfly uses almost sexual language to do so. She describes a foreign man taking a pin and sticking a butterfly to a board, an image that sounds more like sexual dominance and romantic possession than entomology. In the opera, images of sexual and romantic possession are woven into images of political subjugation.