Set in Sylvan, South Carolina in 1964, The Secret Life of Bees tells the story of 14-year-old white girl, Lily Melissa Owens, whose life has been shaped around the blurred memory of the afternoon her mother was killed. She lives in a house with her abusive father, whom she refers to as T. Ray. They have a no nonsense maid, Rosaleen, who acts as a surrogate mother for Lily. The book opens with Lily's discovery of bees in her bedroom. Then, after Rosaleen is arrested for pouring her bottle of "snuff juice" on three white men, Lily breaks her out of the hospital and they decide to leave town. They begin hitch-hiking toward Tiburon, SC, a place written on the back of an image of the Virgin Mary as a black woman, which Deborah, her mother, had owned. They spend a night in the woods with little food and little hope before reaching Tiburon. There, they buy lunch at a general store, and Lily recognizes a picture of the same "Black Mary" but on the side of a jar of honey. They receive directions to the origin of that honey, the Boatwright residence. They are introduced to the Boatwright sisters, the makers of the honey: August, May and June, who are all black. Lily makes up a story about being an orphan. Lily and Rosaleen are invited to stay with the sisters.
They learn the ways of the Boatwrights, as well as the ways of bee keeping. With a new home and a new family for the time being, Lily learns more about the Black Madonna honey that the sisters make. She begins working as August's bee keeping apprentice to repay her for her kindness, while Rosaleen works around the house. Lily finds out that May had a twin sister, April, who committed suicide with their father's shotgun when they were younger. She watches June's ongoing flirtations with, and refusals of marriage to, her boyfriend Neil. Lily and Rosaleen also get to see the sisters' form of religion. They hold service at their house which they call "The Daughters of Mary." They keep a statue of "Black Mary" or "our lady of chains" which was actually a figurehead from the bow of an ancient ship and August tells the story of how a man by the name of Obadiah, who was a slave, found this figure. The slaves thought that God had answered their prayers asking for rescue, and "to send them consolation" and "to send them freedom". It gave them hope and the figure had been passed down for generations.
Lily meets Zach, August's godson. They soon develop intimate feelings for each other. They share goals with each other while working the hives. Both Lily and Zach find their goals nearly impossible to meet but still encourage each other to attempt them. Zach wants to be the "ass-busting lawyer", which means he would be the first black lawyer in the area. Lily wants to be a short story writer.
Lily attempts to tell August the truth but is interrupted by Zach, who takes her for a honey run. They stop at a store to pick up a few things. Zach gets arrested after one of his friends, who they had met at the store, throws a coke bottle at a white man and none of them will tell who did it. Zach and his friends are arrested and put in jail. The Boatwright house decides not to tell May in fear of an unbearable emotional episode. The secret does not stay hidden for long and May becomes catatonic with depression. May leaves the house and August, June, Lily and Rosaleen find her lying dead in the river with a rock on her chest, an apparent suicide.
A vigil is held that lasts four days. In that time, Zach is freed from jail with no charges and black cloth is draped over the beehives to symbolize the mourning. May's suicide letter is found and in it she says, "It's my time to die, and it's your time to live. Don't mess it up." August interprets this as urging June to marry Neil. May is later buried. Life begins to turn back to normal after a time of grieving, bringing the Boatwright house back together. June after several rejections, agrees to give her hand in marriage to Neil. Zach vows to Lily that they will be together someday and that they will both achieve their goals.
Lily finally finds out the truth about her mother. August was her mother's nanny, and helped raise her. After her marriage to T. Ray began to sour, Deborah left and went to stay with the Boatwrights. She eventually decided to leave him permanently and returned to their house to collect Lily. While Deborah was packing to leave, T. Ray returned home. Their ensuing argument turned into a physical fight during which Deborah got a gun. After a brief struggle, the gun fell to the floor, which Lily picked up and the gun accidentally discharged, killing Deborah.
While Lily is coming to terms with this information, T. Ray shows up at the pink house to take her back home. Lily refuses, and T. Ray flies into an enraged rampage. He has a violent flashback which brings him around. August steps in and offers to let Lily stay with her. T. Ray gives in and agrees. However, right before T. Ray leaves the Boatwright house, Lily asks him what really happened the day her mother died. T. Ray confirms that she did do it.
- Lily Melissa Owens: the 14 year old narrator of the story. Lily is the only child of Deborah and T. Ray Owens. Lily loves to read.
- T. Ray Owens: the abusive father of Lily and the widower of Deborah Fontanel Owens.
- Deborah Fontanel Owens: the deceased mother of Lily Owens and wife of T.Ray Owens. Deborah died in a gun accident when Lily was 4. Deborah is buried in Virginia.
- Rosaleen Daise: the African American maid of Lily's household and other neighbors, also acts as Lily's protector and surrogate mother. She is Lily's best friend for most of the book.
- August Boatwright: the eldest of the Boatwright sisters, a beekeeper, a well-respected businesswoman in the community. August is Deborah's best friend.
- June Boatwright: the sister of May Boatwright and August Boatwright. She is a school teacher and musician. June is more serious than August and May.
- May Boatwright: the sister of August and June Boatwright. She had a twin sister, April, who died when she was younger, and as a result of April's death she is super sensitive. May eventually commits suicide.
- Zachary "Zach" Taylor: August's godson who helps her with the hives. He is a football player who attends the local black high school. He wants to become a lawyer. Zach is Lily's main love interest.
- Neil: the principal at the school where June teaches. He has proposed multiple times to June. He eventually becomes June's fiance.
- The Daughters of Mary: Cressie, Queenie and her daughter Violet, Lunelle, Mabelee, and Sugar-Girl who attends with her husband, Otis, the one man of the group. They are followers of Our Lady of Chains.