The musical begins with Rona Lisa Peretti entering the gymnasium to set up. As she passes by the microphone, she has a flashback to the moment when she won the third annual spelling bee by correctly spelling syzygy. The spellers are introduced as they enter, and sing about their anticipation of the bee ("The Twenty-Fifth Annual Putnam County Spelling Bee"). Rona then welcomes the audience to the bee, and calls the selected audience spellers to the stage. She also calls up Olive Ostrovsky, who has not paid the entrance fee yet. When asked if she has a parent in the audience who can pay, Olive reveals that she has arrived by herself on the bus. Rona lets the fee slide for the moment. She then introduces the official word reader, Douglas Panch, who is returning from a five-year hiatus. Panch alludes to an incident five years ago, but declares that he is in a much better place now. Panch introduces the intimidating-looking comfort counselor, Mitch Mahoney, who is doing this as his court-mandated community service. Mahoney leads the spellers (now including the audience spellers) in the Pledge of Allegiance. Panch then explains the rules of the spelling bee ("The Spelling Rules / My Favorite Moment of the Bee 1")
The spelling bee begins, and as each non-audience speller is called forward, the audience learns about his or her background through flashbacks (with other characters in the flashbacks being played by the other spellers on stage, including simple nonspeaking roles played by the audience spellers, as guided by the actors). Olive is shown to be shy and reserved, a result of her uninterested parents — her mother is in India on a spiritual journey, and her father is missing the bee to work late, as usual. She has come to love spelling by reading the dictionary in her home ("My Friend, the Dictionary").
When Leaf Coneybear is called to spell the first time, it is revealed in a flashback that he came in third at his regional bee, but advanced to the county finals when the winner and runner-up had to attend the winner's Bat Mitzvah. His word is capybara, which he has no idea how to spell, but he ends up spelling it correctly while in a trance with an unknown cause.
When William Barfée is called to spell for the first time, Rona describes his unusual technique — he spells the word out on the ground with his foot to get a visual before speaking it. He demonstrates his confidence by returning to his seat immediately after spelling his word, and responding "I know" when Panch says that it is correct.
After a particularly easy word is given to an audience speller, the spellers erupt in "Pandemonium" and rant about how the element of luck makes the bee unfair.
When Leaf is called the second time, he receives acouchi, which he again does not know how to spell. He reminisces about how his family repeatedly calls him "dumb", a sentiment that has sunken in and that he has come to believe. Again, in a trance, he spells the word correctly ("I'm Not That Smart").
Barfée is called again, and this time sings about his technique ("Magic Foot").
Chip Tolentino then is called, but he is not paying attention. Rather, he is fantasizing about Leaf's attractive sister, Marigold, in the audience. He is snapped out of his daze, but is reluctant to take his turn because he has an erection that is showing. Under threat of disqualification, he takes his turn, but his thoughts (aided by the vaguely erotic word that he is given, tittup) distract him and he misspells the word. He catches himself misspelling the word, and backs up to save himself. Unfortunately for Chip, "if you start to spell a word you may start over, but the sequences of letters already spoken may not be changed," as the rules state. He begs for another chance, but Mitch eventually hauls him off ("Pandemonium (Reprise) / My Favorite Moment of the Bee 2").
At this point, the last audience speller is eliminated (he or she simply is called repeatedly in succession and given increasingly difficult words). Mitch sings a special serenade to this audience member for making it this far ("Prayer of the Comfort Counselor").
The remaining spellers (all of the normal cast spellers except for Chip) go on break, and Chip passes through the audience selling snacks, the punishment for being the first eliminated. He explains to the audience why he lost ("My Unfortunate Erection (Chip's Lament)"). Barfée taunts Chip, who throws a bag of peanuts M&M's at him. Allergic to peanuts, he has Olive pick them up for him. Olive and Barfée converse awkwardly, and Barfée begins to develop a crush on Olive.
With the break over, Rona introduces the finalists as they reenter. Last to be introduced is Logainne, who describes her two overbearing fathers and the stress that they put on her ("Woe is Me"). In a rapid montage sequence, the bee is shown progressing through many rounds, ending with Leaf’s elimination on the word chinchilla. He walks away head held high, having proven to himself, despite his elimination, that he is smart (I'm Not that Smart (Reprise)").
Marcy is called to spell, and Rona, who has been announcing factoids about the spellers all along, announces that Marcy speaks five languages. Marcy corrects her, saying, "I Speak Six Languages". She reveals more about her stressful life, where she is pushed to succeed in everything, which she does not enjoy. She is given the word camouflage, to which she sighs, "Dear Jesus, can't you come up with a harder word than that?" Jesus Christ then appears to her and teaches her that she is in control of her own life. Resolved to do what she wants, not what is expected of her, she intentionally misspells the word and exits excitedly ("Jesus / Pandemonium (Reprise #2)").
Olive's cellular telephone rings — it is her father, who she has been anxiously hoping would arrive. She is not allowed to answer the telephone, but she persuades Rona to answer the call for her. Bothered by the breach of the rules, Panch loses his temper and lashes out at Logainne, who is up to spell. Mitch wrestles Panch out, and in the ensuing chaos, Logainne is left alone in the gymnasium. One of her fathers jumps onstage to calm her down, and he pours some of his soda on the floor to make Barfée's foot stick and thus disrupt his technique.
With Panch calmed down, everyone returns to the gymnasium, and Olive is called to spell. She asks what her father had said, and is saddened to learn that he said he is running even later than planned. Her word is chimerical, and mirroring the word's definition, she imagines her parents’ being there and giving her the love that she always has wanted and yearned for ("The I Love You Song").
Barfée is called to spell next, and, when using his signature technique, his foot sticks. However, he is able to spell his word correctly anyway. Logainne is next, and she overcomplicates her word vug and misspells it ("Woe is Me (Reprise)"). Rona is excited that it has come down to the final two ("My Favorite Moment of the Bee 3").
The finals are shown quickly through another montage ("Second"), and Olive and Barfée continue to grow closer, in part by taunting Panch for his earlier outburst. Eventually, Olive misspells a word (elanguescence), giving Barfée a chance to win by spelling his next word correctly. He is torn between winning and letting his Olive win, but with Olive's encouragement, he spells his word correctly (Weltanschauung). Panch awards Barfée the trophy and two hundred dollar prize, and in a surprise act of charity, gives Olive a fictitious runner-up prize of twenty-five dollars from his own pocket — exactly the amount needed to cover her entrance fee. Olive congratulates and hugs Barfée, and each character reads their epilogue, a sentence or two about what they do in the years and decades after the main action of the play ends ("Finale").