The opera is set in 16th century Germany, and is in five acts.
Act I takes place in Faust's 'cabinet'. Faust attempts to kill himself (twice) with poison but stops each time when he hears a choir. He curses science and faith and asks for infernal guidance. Méphistophélès appears (duet: Me voici) and, with a tempting image of Marguerite at her spinning wheel, persuades Faust to buy Méphistophélès's services on earth in exchange for Faust's in Hell.
Act II occurs at the city gates. A chorus of students and soldiers and villagers sing a drinking song, Vin ou Bière. Valentin, leaving for war with his friend Wagner, entrusts the care of his sister Marguerite to his friend Siébel. Méphistophélès appears and sings about the Golden Calf (Le veau d'or). Méphistophélès maligns Marguerite, and Valentin tries to strike him with his sword, which shatters. Valentin and friends use the cross-shaped hilts of their swords to fend off what they now know is an infernal power (chorus: De l'enfer). Méphistophélès is joined by Faust and the villagers in a waltz Ainsi que la brise légère. Marguerite refuses Faust's arm out of modesty.
Act III takes place in Marguerite's garden. Siébel leaves a bouquet for Marguerite (Faites-lui mes aveux). Faust sends Méphistophélès in search of a gift for Marguerite and sings a cavatina Salut, demeure chaste et pure about nature. Méphistophélès brings a trunk of jewels. Marguerite enters, pondering her encounter with Faust at the city gates, and sings a ballad about the King of Thulé, Il était un roi de Thulé, Marthe, Marguerite's neighbour, says the jewels must be from an admirer. Marguerite tries on the jewellery and sings her famous aria, the Jewel Song (Ah! je ris de me voir si belle en ce miroir). Méphistophélès and Faust join the women in the garden and romance them. Marguerite allows Faust to kiss her (Laisse-moi, laisse-moi contempler ton visage), but then asks him to go away. She sings at her window for his quick return, and Faust, listening, returns to her.
In Act IV, in Marguerite's room. Impregnated and abandoned by Faust, Marguerite has given birth and is a social outcast. She sings an air at her spinning wheel (Il ne revient pas). Siébel stands by her. Marguerite goes to the church and tries to pray there but is stopped, first by Méphistophélès and then by a choir of devils. She finishes her prayer, but faints when she is cursed again by Méphistophélès. Méphistophélès sings a lover's serenade under Marguerite's window (Vous qui faites l'endormie). Valentin returns and asks who debauched his sister. Faust and Valentin duel and Valentin is killed. With his dying breath he condemns Marguerite to Hell.
Act V is set in the Harz mountains on Walpurgisnacht. Méphistophélès and Faust are surrounded by witches (Un, deux et trois). Faust is transported to a cave of queens and courtesans, and a feast is held. (If included, the ballet takes place at this point.) Faust sees a vision of Marguerite and asks for her. Méphistophélès helps Faust enter the prison where Marguerite is being held for killing her child. They sing a love duet Oui, c'est toi que j'aime. Mephistopheles returns to urge Faust to hurry, and Marguerite recognizes him as the devil. She calls for divine protection as Faust urges her to hurry away with him and Mephistopheles tells them both that time is running out. Marguerite listens to neither of them, and sings an invocation to angels ("Anges purs, anges radieux"). At the end she hallucinates that Faust's hands are covered in blood, repulses him, and faints; while Mephistopheles cries out that Faust has been judged. Faust prays, while Marguerite's soul rises to heaven (Christ est ressuscité).