It is 1964, and fourteen-year-old Lily Owens is watching the bees fly around her room and thinking back over the events of the summer. These events are narrated in flashback, beginning with the first of July. The narrator lives with her father, a bitter, unkind man named T. Ray, in the town of Sylvan, South Carolina. Her mother, Deborah, died in an accident when Lily was four years old. Lily remembers holding a gun on that day and blames herself for her mother’s death, but her memory of what happened is unclear. One of the few personal possessions she has to remind her of Deborah is a picture of the Virgin Mary with the words “Tiburon, South Carolina” written on the back of it.

The Owens family’s maid is called Rosaleen, and she has been like a mother to Lily since Deborah’s death. After Rosaleen, who is Black, is assaulted and injured by three white men, Lily and Rosaleen decide to run away and go to Tiburon, to find out whatever they can about Deborah while escaping from their current situation.

When they reach Tiburon, Lily and Rosaleen see the same picture of the Virgin Mary that Lily’s mother left behind on the label of a jar of honey at the local store. They discover that this honey comes from the apiary of the Boatwrights, a Black family who live in the town, and go to visit them. The three Boatwright sisters, August, June, and May, invite Lily and Rosaleen to stay with them.

Lily is particularly drawn to August, the eldest of the Boatwright sisters, a thoughtful, intelligent woman who spends most of her time looking after the bees. August tells Lily stories, which she does not always understand. One is about a nun who leaves her convent and returns years later, only to find that the Virgin Mary has been working there in her place. Along with the other Boatwright sisters, August holds weekly religious meetings for a group of women called the Daughters of Mary.

Lily also meets Zach, a boy who helps August with her apiary. Zach is handsome and clever, and Lily finds herself developing strong feelings for him. While she is visiting the office of Clayton Forrest, an attorney who is a friend of Zach’s, Lily makes a telephone call to her father. He demands to know where she is, but Lily refuses to tell him. She asks him to tell her what her favorite color is to demonstrate that he knows anything about her and hangs up the phone when he ignores the question.

May, the youngest of the three Boatwright sisters, once had a twin sister called April, who died by suicide. Since then, May has been emotionally disturbed and has acquired numerous strange habits. One of these is feeding marshmallows to cockroaches. However, Lily recalls that her mother also used to do this and asks May if she knew Deborah. May replies that Deborah stayed with the Boatwright family a long time ago. Lily decides to ask August about Deborah, but before she has a chance to do so, Zach is arrested and jailed for his involvement in a fight with three white men. May is crushed by the news of his arrest and drowns herself.

Zach is acquitted, due to the efforts of Clayton Forrest. Lily tells him how she feels about him, but Zach says that, though he does like Lily, he will not date a white girl. He tells Lily about his ambition to become a lawyer, like Clayton, so that he can oppose racism in the courts. After the Boatwrights have held a vigil in memory of May, Lily asks August to tell her about Deborah. August says that she was the maid in Deborah’s family when Deborah was a child. She asked Lily to stay with her because she knew immediately that Lily was Deborah’s daughter. When Lily was very young, Deborah was so unhappy in her marriage that she ran away, leaving Lily behind, and came to stay with the Boatwrights in Tiburon. After a while, she returned to Sylvan so that she could take Lily with her and leave T. Ray permanently, and it was then that she died.

Lily finds it difficult to forgive Deborah for abandoning her, even though she returned for her later. However, she reflects that she has now found a loving family in the Boatwrights, along with good friends in Tiburon, and her resentment gradually diminishes.

Meanwhile, T. Ray has traced Lily to Tiburon through the telephone call she made from the lawyer’s office. He comes to the Boatwright house and demands that she return to Sylvan, but Lily refuses. The Boatwrights and their friends, the other Daughters of Mary, back her up, and T. Ray is forced to leave. As he does so, he reveals that Lily shot Deborah by accident when she was four years old.

Lily decides to stay with the Boatwrights and is enrolled in the local high school with Zach. She writes about the things that have happened to her and concludes that, although she lost her mother at a young age, she now has many mothers, including August, Rosaleen, and the Virgin Mary.