Vianne and her six-year-old daughter Anouk drift across Europe following the north wind, like Vianne's mother before her. In 1959 they arrive in a quiet French village, overseen by mayor the Comte de Reynaud, at the start of Lent. Vianne opens a chocolate shop; despite not fitting in well with the townspeople, she begins to make headway with some of the villagers, getting them to come to her shop. Reynaud, who will not admit his wife has left him, speaks out against Vianne for tempting the people during Lent.
Armande, Vianne's elderly landlady, is one of her first allies. Armande's daughter Caroline will not let her see her grandson Luc, as she is a "bad influence". Vianne arranges for him and his grandmother to meet in the chocolaterie, where they bond. After finding out about their secret meetings, Caroline reveals her mother is diabetic, but she continues to eat the chocolate when visiting the shop.
Vianne develops a friendship with Josephine, who is being physically abused by her husband Serge, the local café owner. Through their friendship, Josephine finds the courage to leave Serge after he beats her, moving in with Vianne and Anouk. As she works at the chocolate shop and learns the craft, her confidence slowly increases. Simultaneously, under Reynaud's instruction, Serge attempts to make amends for his abusiveness, eventually asking Josephine to come back to him, but she refuses. Later that night, a drunken Serge breaks into the shop, attacking both women, but Josephine knocks him out.
As the rivalry between Vianne and Reynaud intensifies, a band of river Romani camp near the village. Although most of the town objects to their presence, Vianne embraces them and a mutual attraction develops between her and the leader, Roux. They hold a birthday party for Armande with villagers on Roux's boat. When Caroline sees Luc dancing with his grandmother, she begins to accept that Armande's influence in her son's life may be positive. Luc takes Armande home after the party, while Josephine and Anouk fall asleep on a boat, which Serge sets fire to, while Roux and Vianne make love on a barge in the river. No one is hurt in the fire, but Vianne is shaken. Armande later dies in her home and is discovered by Luc. This devastates both Luc and his mother. Meanwhile Roux packs up and leaves with his group.
Reynaud initially believes the fire was divine intervention until Serge confesses to starting it, saying he thought it was what Reynaud wanted. Horrified, Reynaud orders him to leave the village and not to come back.
With the return of the north wind, Vianne decides she cannot win against Reynaud, and decides to move on. Anouk, now attached to the town, refuses to go, and during a scuffle, the urn containing Vianne's mother's ashes breaks, scattering them over the floor. While recovering the ashes, Vianne sees a group of her friends who have come to help out in her shop, and understands the positive influence she has had on their lives. She decides to stay.
Despite shifting sentiment in the town, Reynaud remains staunch in his abstinence from chocolate. On the Saturday evening before Easter, Reynaud sees Caroline, to whom he is attracted, leaving the chocolaterie and is devastated. He breaks into the shop that night, smashing the special window display for the Easter festival. After a morsel of chocolate falls on his lip, he devours much of the chocolate in the window before collapsing in tears and falling asleep. The next morning, Vianne wakes him and gives him a drink to help him recover. Reynaud apologizes for his behavior. Père Henri, the town's young priest, gives a sermon emphasizing the importance of humanity over divinity.
The narrator, a grown-up Anouk, reveals that the sermon and festival are a success. Reynaud and Caroline start a relationship half a year later. Josephine takes over Serge's café, renaming it Café Armande. The north wind returns, but this time Vianne throws her mother's ashes out into the wind. Anouk concludes the story: Roux returns in the summer to be with Vianne and Anouk.
