Recently discharged from service in World War II and surviving on a government pension for unspecified battle wounds, Hazel Motes returns to his family home in Tennessee to find it abandoned. Leaving behind a note claiming a chifforobe as his private property, Motes boards a train for Taulkinham. The grandson of a traveling preacher, Motes grew up struggling with doubts regarding salvation and original sin; following his experiences at war, Motes has become an avowed atheist and intends to spread a gospel of antireligion. Despite his aversion to all trappings of Christianity, he constantly contemplates theological issues and finds himself compelled to purchase a hat and suit that cause others to mistake him for a minister.
In Taulkinham, Motes initially finds an address in a bathroom stall and seeks out Leora Watts, a prostitute. He walks into her house, sits on her bed, and places his hand on her shoe without speaking to her first. He befriends Enoch Emery, a profane, manic, 18-year-old zookeeper forced to come to the city after his abusive father kicked him out of their house. Emery introduces Motes to the concept of "wise blood," an idea that he has innate, worldly knowledge of what direction to take in life, and requires no spiritual or emotional guidance.
Together, Emery and Motes witness a blind preacher and his teenage daughter crash a street vendor's potato peeler demonstration to advertise for their ministry. The preacher introduces himself as Asa Hawks and his daughter as Sabbath Lily Hawks; Motes finds himself drawn to the pair, which Hawks attributes to a repressed desire for religious salvation. Angry, Motes begins shouting blasphemies to the crowd and declares that he will found his own anti-God street preaching ministry. Motes' declarations are lost on everyone except for Emery, who becomes infatuated with the idea.
After Leora destroys his hat for her own amusement, Motes moves into the boarding house where Asa and Sabbath Lily live. Motes becomes fixated on the 15-year-old Sabbath Lily and begins spending time with her. Asa has Sabbath Lily give Motes an old newspaper clipping announcing his intention to blind himself with quicklime at a revival meeting in order to detach himself from worldly pursuits. Initially intending to seduce Sabbath Lily in order to corrupt her spiritual purity, Motes discovers that she is in fact interested in him.
Now skeptical of her and of her father's entire ministry, Motes slips into Hawks' room one night and finds him without his sunglasses on, with perfectly intact eyes: Hawks had faltered when he had attempted to blind himself because his faith was not strong enough, and ultimately left the ministry to become a con artist. His secret found out, Asa flees town, leaving Sabbath Lily to fend for herself. The 15-year-old moves in with Motes, and he begins to more aggressively pursue his ministry, purchasing a dilapidated car to use as a mobile pulpit.
Meanwhile, Emery, believing that Motes' church needs a worldly "prophet," breaks into a museum attached to the zoo where he works and steals a mummified dwarf, which he begins keeping under his sink. He ultimately presents it to Sabbath Lily to give to Motes on his behalf; when Sabbath Lily appears to Motes cradling it in her arms in a parody of the Madonna and Child, Motes experiences a violent revulsion to the image and destroys the mummy, throwing its remnants out the window.
Inspired by Motes' fledgling street ministry, local con artist Hoover Shoats renames himself Onnie Jay Holy and forms his own ministry, the "Holy Church of Christ Without Christ," which he encourages the disenfranchised to join for a donation of $1. The absurdity amuses passersby and they begin to join as a joke. This angers Motes, who wants to legitimately and freely spread his message of antireligion. Despite Motes' protests, Holy moves to the next level in promoting his ministry, hiring a homeless, alcoholic man to dress up like Motes and act as his "Prophet."
During a rainstorm, Emery seeks refuge under a theater marquee, and learns that as a promotion, a gorilla will be brought to the theater to promote a new jungle movie. An excited Emery stands in line to shake the gorilla's hand, but is startled to find that the gorilla is actually a man in a costume who, unprovoked, tells Emery to "go to hell." The incident causes Emery's "wise blood" to give him some inarticulated revelation, and he seeks out a program of the "gorilla's" future appearances. That night, Emery stalks the man to another theater, stabs him with a sharpened umbrella handle, and steals his costume. Enoch takes the costume out to the woods, where he strips naked and buries his clothes in a shallow "grave" before dressing up as the gorilla. Satisfied with his new appearance, he comes out of the woods and attempts to greet a couple on a date by shaking their hand. Emery is disappointed when they flee in terror, and finds himself alone on a rock overlooking Taulkinham.
Back in town, Motes angrily watches as Holy begins to grow rich from his new ministry. One night he follows Holy's "prophet" as he drives home in a car resembling Motes's. He runs the car off the road. When the man exits the car, the stronger, more forceful Motes threatens him and orders him to strip. The man begins to comply, but Motes is overcome by a sudden rage and repeatedly runs the man over. Exiting the car to ensure he is dead, Motes is startled when the dying man begins confessing his sins to Motes.
The next day, Motes is pulled over by a strange policeman with unnaturally blue eyes, who claims to be citing him for driving without a license. He orders Motes to drive to a nearby cliff, orders him out of the car, then, remarking that someone without a license doesn't need a car, pushes it off the cliff. The incident, coupled with the false prophet's death, causes Motes to become sullen and withdrawn. Motes purchases a tin bucket and sack of quicklime and returns to the boarding house. Completing the action that Hawks couldn't finish, he blinds himself with the quicklime.
During an extended period of living as an ascetic at the boarding house, he begins walking around with barbed wire wrapped around his torso and sharp rocks and pebbles in his shoes. After paying for his room and board, he throws away any remaining money from his military pension. Believing that Motes has gone insane, the landlady, Mrs. Flood, hatches a plot to marry him, collect on his pension, and have him committed to an insane asylum. In attempting to seduce Motes, Mrs. Flood instead falls in love with him. After she suggests to Motes that they marry and she care for him, Motes wanders off into a thunderstorm.
Motes is found three days later, lying in a ditch and suffering from exposure. Angry at being asked to return what they believe is a mentally ill indigent, one of the cops who find Motes strikes him in the head with his baton. Motes dies in the police car on his way back to the boarding house. When the dead Motes is presented to Mrs. Flood, she mistakenly thinks he is still alive. She has him placed in bed and cares for his lifeless corpse, telling him he can live with her for as long as he likes, free of charge. Looking into his empty eye sockets, Mrs. Flood thinks she sees a light twinkling inside them.
