The movie opens in 1964, during the civil rights movement. Lily is almost fourteen years old and has an abusive father and no mother. In the first scene, a woman in a dress wanders around a room and goes back and forth in a closet. A marble rolls on the ground and a little girl is playing with a clear glass shooter marble and a mirror. The mother, Deborah Owens (Hilarie Burton) is taking clothes from the closet and putting them into a suitcase. Suddenly a man barges in and starts to rage at her, saying that she isn't going to leave him. He throws the suitcase onto the ground and grabs her roughly. The woman reaches for a gun in the closet and points it at the man, telling him that she just wants to go. The man wrestles the gun out of her hand and it falls on the ground. The child's hand goes to pick up the gun. The gun goes off and the scene fades to an older Lily lying in bed, her eyes open.
"I killed my mother when I was four years old. That's what I knew about myself. She was all I wanted and I took her away. Nothing else much matters," says Lily's voice over.
In the middle of the night, Lily sees hundreds of bees in her room and runs to tell her father, T. Ray (Paul Bettany), who yells at her to go back to bed. Frustrated, Lily runs into their peach orchard and digs up a box she buried there. The box contains her mother's gloves, a small photograph of her mother, and a scrap of wood with a picture of the Virgin Mary on it. Lily puts on her mother's gloves, partially unbuttons her blouse, and holds the photograph close to her heart. While she lies on the soft dirt, staring at the stars, she hears her father calling her. Hurriedly, she takes off the gloves and slips the items back into the box and starts to bury it. While she is buttoning her blouse, her father approaches her and yells for "whoever was out there with her". He grabs her arm and runs her into the house, then shouts, "You tryin' to get yourself pregnant?!" He pours a box of grits onto the floor and without further speech, Lily kneels onto the grits. Her father sits in a chair watching her and drinking a beer.
The next morning, Rosaleen, their Negro housekeeper, is sweeping up the grits. She asks Lily how long she was on the grits. Lily replies that she was there for an hour. As Lily sits down, Rosaleen surprises her with a cake for her 14th birthday. As T. Ray walks into the room, Rosaleen states that she is going to take Lily into town to buy her a training bra. T. Ray reluctantly hands her money and quietly says "Happy birthday" as he walks out of the room. On TV they all see that the Civil Rights Bill was passed.
When Rosaleen and Lily start to walk downtown, they are confronted by four bigots who call Rosaleen some bad names, and in return, Rosaleen pours her jar of spit on their feet. Unwilling to apologize, she is beat up by them and screaming, Lily is held back.
After T. Ray and Lily get back home, Lily says, "You know most girls would want toys or whatever for their birthday, but I was thinkin' . . . maybe you could tell me 'bout my mother instead." T. Ray replies that her mother would spend hours luring bugs out of the house with "graham crackers and marshmallows and stuff", but he would always just kill 'em. He then looks down to see a roach crawling across the floor, and steps on it.
Lily still demands to know more about her, and her father replies that she left and when she came back, she got all of her stuff but she wanted to leave Lily behind. When Lily calls him a liar, he is furious and tells her to stay in her room. When he leaves the house, Lily leaves a letter saying ". . . don't even bother to look for me . . . " and leaves. She goes to the "colored ward" of the hospital and finds Rosaleen. Together they run away to a town where Lily's mother was thought to have once lived. There in a store they find a honey jar with the same picture of the Virgin Mary as was on the slab of wood that Lily retained. When they ask the store owner who made this honey, he leads them to the home of August Boatwright and her sisters, May and June. May used to have a twin, April, who is revealed to have died later in the movie.
Lily experiences growing up in their household and for the first time ever, lives with a real, loving, caring family making honey and being a part of each others' lives.
Later on, May gets so depressed she drowns herself by placing a large rock upon her chest and laying down in a shallow pool.
August and her sisters decide to change Rosaleen's name to July.
Lily shows August the picture of her mother, and August instantly recognizes her as "Deborah". As August and Lily discuss Deborah, Lily confesses that while trying to help her mother, she ended up killing her, after which she breaks down crying and runs to her room. Screaming, she throws several jars of honey at the wall, smashing them.
T. Ray comes to the Boatwrights' looking for Lily. He then gives August permission to take care of Lily for as long as she wants to stay there. As T. Ray drives off, he admits that the day Deborah left, she wasn't only coming back for her stuff, but coming back for Lily. He says he lied because she wasn't coming back for him.
Lily's voice over states that she thought, as T. Ray drove off saying, "Good riddance," that he was really saying, "Lily, you'll be better off here with all of these mothers."