It is 1964 in Sylvan, South Carolina, and Lily Melissa Owens, a fourteen-year-old white girl, lives on a peach farm with her father, T. Ray, who is both neglectful and abusive. Lying in bed in her room at night, Lily is often visited by bees that seem to be at home with her. Lily holds a terrible and guilty secret: She believes she shot and killed her mother, Deborah, when Lily was four years old. Her vague memory of that day — when her parents were arguing and she picked up and shot the gun that her mother had dropped — continues to haunt her, and she yearns to know more about her mother.
Lily has a housekeeper/nanny named Rosaleen Daise, who has cared for Lily for ten years. When Rosaleen watches President Johnson sign the Civil Rights Act on television, she decides she will register to vote. She and Lily walk into town but are accosted by three white men who harass Rosaleen. Rosaleen angrily pours the contents of her snuff jar on their shoes, and the men beat her right in front of Lily. The police arrive and arrest Rosaleen, taking her and Lily to jail. When T. Ray comes to pick Lily up, he is angry and berates her for such stupid behavior. He also scares her when he explains that Rosaleen may be killed by the men she insulted. This terrifies Lily because she loves Rosaleen. Once home, Lily stands up to her father during an argument, and T. Ray hurts her by saying that ten years ago her mother was only coming back to get her clothes; that is, that she had planned to abandon Lily. Earlier, Lily captured some bees in a jar, and now she sees they have escaped. Like the bees, she also plans to escape, leaving behind her abusive father and freeing Rosaleen.
When T. Ray leaves temporarily to work on his workers' payroll, Lily sneaks away, carrying with her a bag of things her mother, Deborah, had left earlier, including a photo of a black Mary, mother of Jesus. Lily manages to free Rosaleen, and they hitchhike to Tilburon, South Carolina, because Deborah had written that town on the back of the picture in Lily's bag. Lily hopes it's a clue to help her find out about her mother. Once they reach Tilburon, Lily sees the exact same picture of Mary on honey jars at a small grocery store. After inquiring about the label, Lily finds it belongs to a local black family of sisters — called the Boatrights — who are beekeepers. Lily and Rosaleen go to the bright pink Boatright house outside of town and are welcomed and taken in. Lily lies about their earlier life and hopes to stay long enough to find out whether her mother was ever there.
August Boatright and her sisters, May and June, have a lucrative honey business on twenty-eight acres of land. June is suspicious of and distant from Lily, and May seems slow and emotional. They also meet Neil, June's boyfriend of many years, who wants to marry June but keeps getting rejected. The other sister, May, is oversensitive to pain, and when she gets upset she must write down the sorrowful thing on a paper and stick it in a crack at her "wailing wall," a wall of stones on the farm. This behavior seems to be connected to the suicide of June's twin sister, April, years earlier. As time passes, Lily helps August with the beekeeping, and Rosaleen keeps an eye on May in the house. Lily is given a room in the "honey house," where she can sort out her feelings. She increasingly likes August but is afraid to tell her the truth about her previous life, for fear that August will reject her. Meanwhile, she develops a crush on Zach, a black teenage worker who helps with the bees.
Lily and Rosaleen become increasingly comfortable in this amazing community of sisters. A group of women called the Daughters of Mary also come to the house, because they all practice a form of homemade religion. It is partly Catholic, including reciting the rosary, and partly a product of slavery. The group displays a wooden ship's statue of a black Mary. The Daughters pray to her, believing she can give them power and lead them to unchain themselves from various social barriers. Lily and Rosaleen join them, and soon Lily realizes the women do not see her as white. The society of women helps August, June, and May encourage Lily to believe in herself and feel loved. But still she cannot tell August the story of her family or earlier life.
Lily becomes increasingly close to Zach and on a trip to work on the bee hives, she feels the first stirrings of sexual awakening. They share their hopes and dreams: Lily's of wanting to become a writer and Zach's of becoming a lawyer. Sensing Lily's lack of self-confidence, Zach gives Lily a journal to record her stories. They go to town and take honey to the law office of a white lawyer who is helping Zach. While Lily is alone in the office, she impulsively calls her father, demanding to know if he even knows her favorite color. He is angry and threatens to find and beat her.
One day, Lily walks into the kitchen and sees May doing something she remembers her mother, Deborah, doing. She confronts May and discovers she knew Lily's mother. Totally shaken, Lily doesn't know what to make of this new information. She decides to face August about it, but before she can, Zach takes her into Tilburon — which is restless because of rumors about a racial confrontation — again to buy parts for his car. The two park the truck at the same time that a group of African-American boys near the truck throw a bottle at a white man. Zach is arrested with the group, and a terrified Lily makes her way back to the Boatright house. They don't want May to know about Zach's arrest because she is so fragile. But Zach calls the house and May answers the phone, finding out about his circumstances. Leaving the house by herself, she commits suicide by drowning in the nearby river.
The next few days are taken up with a period of mourning and the funeral. Zach is released from jail on the testimony of an eyewitness. A celebration of the Mary statue ensues for two days, and during a walk, Zach and Lily kiss and he promises that, despite their races, they will be together some day. Neil and June set a date to be married after May left a note reminding June that life goes by too quickly to throw their love away.
Once the mourning and celebration are over, Lily waits in August's room to tell her the true story of her family. Surprisingly, she discovers that August already knows who she is. August reveals that she worked as a housekeeper and nanny years earlier for Deborah's family. She explains the story of Deborah's marriage to T. Ray and how, after she had Lily, she suffered a nervous breakdown and came to stay with August for a few months, leaving Lily behind. Her picture of T. Ray's love for Deborah and his loss is a viewpoint Lily had never considered before. August says Deborah was arranging for a divorce and a trip back to get Lily so they would live together in Tilburon. Lily explains to August that she accidentally killed her mother, and that she is unlovable. But August begs her to forgive her mother for not being perfect and forgive herself for an action she didn't understand.
Lily spends the next few days angry and bitter about her mother leaving her to go to August's. She nearly destroys the honey house with her grief and rage. But as she thinks about August's words, she begins to acknowledge that her mother loved her and came back for her. August gives Lily some of Deborah's belongings, including a photo of Deborah feeding a baby Lily, which Lily takes as the sign of her mother's love, for which she has waited most of her life.
T. Ray shows up at the Boatright house, having traced Lily's call from the lawyer's office. He and Lily have a terrible argument, and T. Ray hits and kicks her. But Lily is able to call him "Daddy" and get him to realize she is not her mother. His pride was wounded when Deborah left, and he has taken his anger out on Lily ever since. August convinces him to let Lily stay with her and, as he leaves, Lily asks him if she truly did kill her mother. He replies, "Yes," but that she didn't mean to, an extraordinary admission.
That fall, Lily goes to school with Zach at the white high school and learns to love herself living with this community of strong, independent women. Through these experiences, Lily has learned to trust her own instincts and matures into a young lady who believes in herself.