Act I
A group of people at a graveyard mourn the passing of Emily Deetz. Emily's daughter, Lydia, reflects on the death of her mother and her own inability to be noticed by her father, Charles ("Prologue: Invisible"). A millennia-old demon named Beetlejuice appears and mocks the idea of living life to the fullest, as it will all be worthless once death comes ("The Whole 'Being Dead' Thing"). Beetlejuice then addresses the audience directly, explaining that, as a demon, he is invisible to all living beings unless he gets a living person to say his name three times, and reveals that he has come up with a plan to accomplish this.

Beetlejuice then introduces Adam and Barbara Maitland. They are a normal married couple who desperately want to start a family, but are not emotionally ready and project their insecurities onto their hobbies. As the Maitlands reason to themselves why they are not ready for a child, they fall to their deaths through unstable floorboards in their home ("Ready, Set, Not Yet"). The Handbook for the Recently Deceased falls from the sky, but Beetlejuice burns it, wanting the newly deceased Maitlands to haunt their house and get a living person to say his name three times. When the Maitlands awaken from their fall and realize that they are dead, Beetlejuice reveals himself to the couple and offers to help them adjust to the Afterlife ("The Whole "Being Dead" Thing, Pt. 2"). He reveals to the Maitlands that a new family, the Deetzes, have bought their house and that in order to remain alone, they will have to scare them away, so the Maitlands accept his help ("The Whole "Being Dead" Thing, Pt. 3").

While moving in, Charles reveals to Lydia that he wants to start a gated community, using the house as a flagship model home, and is holding a dinner party with some business friends. Lydia expresses her desire for her mother to return, mentioning the fact that nobody seems to care that she is gone. Praying for her to send a sign that she is still there, Lydia vows to make her father acknowledge the fact that tragedy struck their family ("Dead Mom"). In the attic, Beetlejuice is trying to teach the Maitlands how to be scary. Despite his best attempts, they prove to be not scary at all ("Fright of Their Lives"). Beetlejuice becomes frustrated with the couple and abandons them, so they vow to scare the Deetz family away themselves ("Ready Set" (reprise)). Meanwhile, Delia, a woman who Charles hired to be Lydia's life coach and his secret lover, tells Lydia how everything happens for a reason, but fails to get her in a positive state of mind ("No Reason"). After their session, Lydia meets the Maitlands as they are roaming the house trying to scare the Deetzes. Lydia wants to leave the house just as much as the Maitlands want her family out, so she tries to convince her dad that the house is haunted, only to find out that he and Delia are engaged.

Feeling as if Charles is just trying to replace her mother, Lydia flees to the roof, where a depressed Beetlejuice laments that he will never be seen ("Invisible" (reprise)). He becomes ecstatic however when he realizes Lydia can see him and tries to convince her not to kill herself, with the intention of getting her to free him from his curse. Lydia teases Beetlejuice, but does not say his name. The Maitlands come to check on Lydia, only to be possessed by Beetlejuice into saying positive things about him to further convince Lydia. Upon learning about possession and that any ghost can do it, regardless of skill, Lydia decides not to work with Beetlejuice and instead work with the Maitlands to ruin Charles' party ("Say My Name").

At the dinner party, Barbara and Adam possess Charles, Delia and their guests ("Day-O (The Banana Boat Song)"). However, instead of being scared, the investors see the ghosts as a selling point; making them more interested in Charles' project. Feeling desperate, Lydia resorts to summoning Beetlejuice. Now visible to the living and able to affect the world around him, he forces the Maitlands to the attic before throwing Charles, Delia and the investors out of the house, much to Lydia's joy.

Act II
A Girl Scout named Skye explains to the audience how she has a heart condition where anything shocking could stop her heart but that she is nevertheless excited to be a Girl Scout. She rings the doorbell of the Deetzes' house and is greeted by Lydia, who invites her inside ("Girl Scout"). However, Beetlejuice appears and frightens the poor girl into leaving. He summons more versions of himself to help Lydia scare every visitor that comes to the house ("That Beautiful Sound"). He also tells Lydia that since she lives and works among the dead now, she should also follow their rules, and gives her a copy of the Handbook for the Recently Deceased. But because she is not dead, Lydia cannot open it. Despite this, she realizes it could help her reunite with her mother, and runs to the attic for Barbara and Adam's help. Feeling alone and betrayed again, Beetlejuice talks with his clones about how he wants to leave the house to finally connect with people now that he can be seen. To achieve this, he decides to trick Lydia into marrying him, which will allow him to roam free in the living world ("That Beautiful Sound" (reprise)).

In the attic, Barbara and Adam help Lydia open the Handbook, when they realize they should have gone straight to the Netherworld instead of remaining in their house. Adam opens the door to the Netherworld, but Barbara shuts it and the Handbook, afraid of leaving the house. Lydia berates them because she hoped to use the book to summon her dead mother and leaves disappointed and angry. Barbara realizes that all of their fear has held her and Adam back, so they decide to become bolder and better people ("Barbara 2.0").

Delia, Charles, and Delia's guru, Otho, re-enter the house to rescue Lydia, bringing a box that can supposedly trap souls. Beetlejuice tricks Lydia by telling her that reading a passage from the book will resurrect her mother, but instead she unknowingly begins to exorcise Barbara and is forced to agree to marry Beetlejuice to stop it ("The Whole "Being Dead" Thing, Pt. 4"). He stops the exorcism and opens a door to the Netherworld to send the Maitlands away for good, but Lydia jumps through the door, with Charles following. Enraged that his plan has failed again, Beetlejuice decides to kill everyone instead ("Good Old Fashioned Wedding").

Lydia and Charles enter the Netherworld and are greeted by Miss Argentina, who along with other Netherworld residents, urges them to return to the living world ("What I Know Now"). They then meet Juno, director of Netherworld Customs and Processing, who soon finds out they are still alive. Lydia runs from Juno and frantically searches for her mother in the Netherworld, but is unable to find her. Charles finds Lydia in distress and reconciles with her ("Home").

The Deetzes return to the house, where Beetlejuice is preparing to kill everyone. Lydia plans to trick him by agreeing to marry him as Charles, Delia, and the Maitlands get the demon ready ("Creepy Old Guy"). The wedding brings Beetlejuice to life, allowing Lydia to stab him and kill him again, making him "Recently Deceased". Lydia and the Maitlands try to send him back to the Netherworld, but Juno appears, reveals herself as Beetlejuice's mother, and tries to take Lydia back with her. Beetlejuice stands up to Juno, having learned to appreciate life in his brief experience. Juno pretends to be moved by Beetlejuice's speech and throws him out of the house. The Maitlands, Charles, and Delia refuse to let Juno take Lydia. Beetlejuice then crashes through the wall riding a sand worm, which eats Juno.

Beetlejuice says his last goodbyes to everyone before leaving. The Deetzes and Maitlands rejoice in their victory and agree to share the house as they clean up and repair the damage. Lydia accepts that although her mother is gone, there is still so much left to enjoy in life ("Jump in the Line").