The film opens in the 1630s New England, centering on William, the patriarch played by Ralph Ineson, who stands trial for heresy. He vehemently insists that those around him are false Christians, while the court accuses him of speaking against God. William's family, which includes his wife Katherine, portrayed by Kate Dickie, their eldest daughter Thomasin, played by Anya Taylor-Joy, son Caleb, portrayed by Harvey Scrimshaw, and the twins Mercy and Jonas, set out to establish their own farm after being expelled from their New England plantation. The twins develop a peculiar friendship with a large black goat they name Black Phillip.
One fateful afternoon, while playing Peek-A-Boo with her baby brother Samuel, Thomasin tragically loses him. When she looks down, she finds that he has vanished. We then witness a chilling scene deep in the woods, where an ancient, haggard woman is seen preparing what seems to be Samuel's remains before disappearing into the darkness. Katherine becomes heartbroken over the baby's disappearance, believing that a wolf is responsible. As Caleb joins William for a hunt, he grows distracted by Thomasin's burgeoning femininity and becomes haunted by the notion that their misfortunes are a punishment for sin.
During their hunting trip, William suffers an injury, which leads them back home where an enraged Katherine awaits. After an unsettling encounter at the river, where Mercy accuses Thomasin of witchcraft, the tension escalates. Thomasin, half-jokingly, claims to be a witch, terrifying Mercy with her words. With their crops failing, she and Caleb venture into the woods, only to become separated. Caleb stumbles upon a small, isolated cottage, leading to a disturbing encounter with a beautiful woman, played by Sarah Stephens, whose intentions are far from innocent.
Eventually, Thomasin finds Caleb in a vulnerable state, prompting the family to fear an evil presence is corrupting them. The children’s terrifying accusations against Thomasin ramp up to a point where even Katherine starts to believe them. As the family prays over an ailing Caleb, he succumbs to what seems like possession, ultimately dying with a smile, much to Thomasin's horror.
Accusations fly, leading William to confine his surviving children in the barn with their goats. There, they witness a horrifying sight involving a pale figure and blood, causing sheer terror. Meanwhile, Katherine, convinced of Thomasin's culpability, approaches what she believes to be Caleb, only to find herself ensnared in a gruesome illusion.
The following day, with the goats slaughtered and the twins missing, a chaotic confrontation occurs between Thomasin and William, which leads to a tragic end for Katherine. In a fit of rage and desperation, Thomasin kills her mother, only to seek solace in a dark pact with Black Phillip. When she finally encounters him, she strips herself of inhibitions, drawn into the woods where she finds a coven of witches, all engaged in an ecstatic dance around a fire. Amidst the chaos, Thomasin embraces the darkness and ascends, floating high above the trees, fully accepting her fate.
