The Bean Trees opens in rural Kentucky. The novel’s protagonist, Taylor Greer, who is known at the beginning of the novel by her given name, Marietta, or by her nickname, Missy, remembers a moment in her childhood when Newt Hardbine’s father was thrown to the top of the Chevron sign after his tractor tire exploded. Ever since then, Taylor has been afraid of tires. Taylor goes on to tell the story of Newt Hardbine, a peer of Taylor’s who died while Taylor was still in high school. Although Newt and Taylor seemed like identical kids when they were small, Taylor was the one to escape small-town life. She did so by avoiding pregnancy, getting a job working at the hospital, and saving up enough money to buy herself an old Volkswagon bug. About five years after high school graduation, Taylor says goodbye to her beloved mother, Alice Greer, and leaves Pittman County, Kentucky, for good.

The protagonist decides that she will drive until her car runs out of gas and then take a new name based on wherever she is when her car stops. She ends up in Taylorville, and changes her name from Marietta to Taylor. Her car breaks down in the middle of the Cherokee Nation in Oklahoma, and she stops in an old bar for a cup of coffee and a hamburger. As she sits in her car, getting ready to leave, a woman approaches and puts a baby in the front seat of Taylor’s car, telling her to take it. She tells Taylor she is the sister of the child’s mother and that the baby was born in a Plymouth car. The woman leaves with no further explanation. Taylor is bewildered, but drives off with the child. They go to a hotel, and while bathing the baby, Taylor discovers that the baby, a girl, has been abused and sexually molested. She names the baby Turtle because the girl clings to things like a mud turtle.

Eventually, Taylor and Turtle make it to Tucson, Arizona. When Taylor’s two back tires blow out, Taylor goes to an auto-repair shop called Jesus Is Lord Used Tires. There she meets the owner, a kind, wise woman named Mattie. Mattie takes to Turtle right away. Taylor moves into a Tucson hotel with Turtle and finds a job working at the Burger Derby.

The narrative switches to the story of Lou Ann Ruiz, another Kentuckian living in Tucson. Lou Ann has been abandoned by her husband, Angel. On January 1, she gives birth to a son, Dwayne Ray. Lou Ann’s mother and Granny Logan come west to visit the baby, and Granny Logan brings water from the Tug Fork River in Kentucky, which she suggests should be used to baptize the baby. When Angel comes home to gather up some of his things, he pours the water down the drain.

Meanwhile, Taylor has started her new job, but she quits six days later. She begins to look for a place to live, and finds a room for rent listed in the paper. The room turns out to belong to Lou Ann. The two women become fast friends, and Taylor takes the room. Without work, Taylor is left with no option but to take a job working for Mattie at Jesus Is Lord Used Tires. One day Taylor meets two of Mattie’s friends, Estevan and Esperanza, a married couple from Guatemala. Soon, it is evident that they are illegal aliens living with other illegal aliens in Mattie’s home above the tire shop.

A month or so later, Taylor takes Turtle to see a doctor and finds that Turtle’s growth has been stunted because she was abused. Turtle is not a baby, as her size indicates, but a three-year-old. That same day, Angel tells Lou Ann that he is leaving her for good.

Mattie’s friend Esperanza attempts suicide. When Estevan comes to tell Taylor this news, he ends up divulging the story of their past. He tells her that he and Esperanza had to leave behind a child in Guatemala. The government wanted the names of union members from Estevan and Esperanza and took their daughter, Ismene, as a way of forcing them to tell. Choosing to save seventeen lives instead of trying to get their daughter back, the couple fled their country. Estevan spends the night on Taylor’s couch. Taylor realizes she is falling in love with him.

After a few weeks, Lou Ann gets a job at a salsa factory, supporting herself in the absence of her husband. No sooner does she start her new job than Angel sends a package with presents for Lou Ann and Dwayne Ray, and a letter asking her to come live with him in Montana, or, if she does not want to do that, to let him come back and live with her in Tucson. After consideration, Lou Ann refuses to take him back.

On the night of the first summer rain, Mattie takes Esperanza, Estevan, and Taylor into the desert to see the natural world come to life. Turtle is left with her baby-sitter, a blind woman named Edna Poppy. Edna and Turtle go to the park, and because of her disability, Edna does not notice when a prowler approaches Turtle. Taylor returns and hears as much of the story as Edna can tell: Edna heard struggling and swung in the direction of the attacker with her cane. She hit him and then felt Turtle tugging on the hem of her skirt. Turtle does not seem hurt, but she has stopped speaking and has the same vacuous look in her eyes that she had when Taylor first saw her. Turtle’s trauma and the difficulties of Estevan and Esperanza make Taylor depressed. To make matters worse, the police investigation into the attack on Turtle reveals that Taylor has no legal claim on Turtle. Taylor will be forced to give her to a state ward or find a way around the law. The social worker in Tucson gives Taylor the name of a legal advisor in Oklahoma, where the laws are different.

Mattie becomes worried about Estevan and Esperanza’s safety. A recent crackdown on illegal immigration will force them to find a new home and a way of getting there. Taylor decides she will transport Estevan and Esperanza to another sanctuary for illegal immigrants in Oklahoma. While there, she will look for Turtle’s relatives and see if they will consent to a legal adoption. Once in Oklahoma, Taylor returns to the bar where she received Turtle but finds that it has changed owners. There are no signs of the people she met there seven months before. Taylor, Esperanza, and Estevan decide to go to the Lake o’ the Cherokees. During that time, Taylor concocts a plan to convince the authorities in Oklahoma that Estevan and Esperanza are Turtle’s biological parents.

Once in the office of Mr. Armistead, the legal authority in Oklahoma, Esperanza and Estevan pretend to be Turtle’s biological parents. Esperanza sobs real tears at the prospect of giving up Turtle, and Taylor realizes that Esperanza is grieving the loss of her own daughter, who looked so much like Turtle. Taylor and Turtle drop off Esperanza and Estevan at their new home, a church in Oklahoma. Taylor says a tearful goodbye to Estevan. Taylor then calls her mother, who comforts her. Taylor and Turtle head back to Tucson, a place that both of them now call home.