The film starts with William (Ralph Ineson), the patriarch of a Puritan family, on trial in 1630s New England. He dismisses those around him as false Christians, and the others claim that he speaks ill of the word of God.In a flashback, William's family includes his wife Katherine (Kate Dickie), eldest daughter Thomasin (Anya Taylor-Joy), son Caleb (Harvey Scrimshaw), twins Mercy (Ellie Grainger) and Jonas (Lucas Dawson), and baby Samuel. They recently moved off their plantation in England to a small farm. Mercy and Jonas frequently play with a large black goat that they named Black Phillip.One afternoon, Thomasin is outside playing Peek-A-Boo with Sam. She covers her face to scare him, but when she looks down, Sam is gone. We cut to somewhere in the darkest part of the woods where a wrinkled hand strokes Sam's body, moments before the creature lowers a knife to his chest. We then see a haggard old woman pounding what appear to be Sam's remains before consuming them. The woman then slowly walks out into the woods.Katherine becomes distraught following Sam's disappearance. The family believes that a wolf took the baby. Caleb goes out to hunt with his father, but first he starts to notice Thomasin's breasts. Out in the woods, Caleb becomes fearful that Sam was taken because he lived in sin, making Caleb worry that he is also leading a sinful life that will lead to his doom.William comforts his son, and they proceed to hunt. William aims his rifle at a rabbit, but the recoil from the shot gets him in the eye, and the rabbit runs away. The two return home to an angry Katherine. Thomasin takes the blame for her father for the two of them going to hunt.Thomasin and Caleb are by the river gathering water. Mercy comes along and accuses Thomasin of being a witch, blaming her for Sam's disappearance. Thomasin plays along with the accusation and starts to terrify Mercy. Thomasin says she is a witch, and that she will get Mercy if she continues to bother her.With a lack of growth on their crops beginning to turn problematic, Thomasin and Caleb venture into the woods. The two are separated from each other. Caleb disappears and comes across a small cottage. From the doorway emerges a beautiful woman (Sarah Stephens). She lures Caleb toward him and she kisses him before grabbing his head with a haggard hand.Thomasin later finds Caleb outside in the rain, naked and scarred. The family becomes worried that something evil is overtaking them. Mercy and Jonas continue to accuse Thomasin of being a witch, to the point where even Katherine appears to believe it. Later, Katherine discusses with William that they should give Thomasin to another family, which she overhears. Caleb is bedridden, and the family prays for him. After a while, Caleb begins to writhe and speak some sort of prayer, while Mercy and Jonas also writhe on the ground as if they were possessed. Caleb speaks as though he accepts that he is about to meet God, and he starts to moan passionately before dying with a smile on his face.Thomasin runs outside to cry in despair. William starts to accuse her of evildoing that led to Caleb's death. She angrily defends herself and states that perhaps it was Mercy and Jonas that made a demonic pact with Black Phillip. William locks his three surviving children in the barn with the goats until something happens. Inside the house, Katherine tearfully confesses to William that she had an affair from which Samuel was born.In the barn, the kids see a pale, nude figure drinking the blood of one of the goats. The creature (a witch) turns around and cackles at Mercy and Jonas, causing them to scream. Meanwhile, Katherine appears to find Caleb sitting in a chair, holding Samuel. She approaches them and takes Sam to breastfeed him, but in reality, it is just a crow picking at Katherine's bosom while she laughs gleefully.In the morning, the goats have been slaughtered, and Mercy and Jonas have vanished. Thomasin emerges from the barn and sees Black Phillip charge at William, impaling him with one of his horns. William grabs a hatchet and seems ready to fight, but he then drops it, allowing Black Phillip to charge at him again and knock him into a pile of logs that crushes him. Katherine comes out and continues to accuse Thomasin, blaming her for the deaths of her family members. Katherine starts to choke Thomasin, who continuously tells her mother that she loves her. Thomasin grabs a nearby blade and hacks at Katherine's face until she is dead.Thomasin quietly walks into a barn and dons a cloak. She later encounters Black Phillip and demands to speak to him. After a brief moment of silence, we hear the quiet voice of Phillip. He asks Thomasin what it is that she desires, and tells her what he can promise to give her. Phillip appears to take human form and walks behind Thomasin, telling her to undress. She does, and she follows him into the woods while naked. In the middle of the woods is a coven of witches, all dancing nude around a fire. The witches then start to float in the air. Thomasin embraces the darkness and begins to float high above the trees herself.