In the fictitious town of Sylvan, South Carolina in 1964, 14-year-old Lily Melissa Owens lives with her abusive father, T. Ray, and her African-American maid, Rosaleen. Much of Lily's life has been shaped around the blurred memory of the afternoon her mother was killed. Lily's discovers 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. The two begin hitch-hiking toward Tiburon, South Carolina, a place written on the back of an image of the Virgin Mary as a black woman, which Deborah, Lily's 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. Rosaleen and Lily receive directions to the origin of the honey, the Boatwright residence. They are introduced to the Boatwright sisters, the makers of the honey: August, May, and June, who are all black. When Lily meets the sisters she makes up a story about being an orphan. Believing Lily's story, August, June, and May invite Lily and Rosaleen to stay with them. 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 died by 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' religious ceremonies. The sisters hold service at their house which they call "The Daughters of Mary." They keep a statue of the "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 enslaved, found this figure. The enslaved men and women 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 eventually 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 attorney 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 goes missing. August, June, Lily and Rosaleen go looking to find her and end up finding her lying dead in the river with a rock on her chest. It looks to be a suicide, due to May's depression from Zach being arrested. 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 Boatwright residence, also known as 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 Lily was the one to, accidentally, kill her mother Deborah.