Thirteen-year-old Theodore Decker survives a terrorist bombing in a New York art museum, which kills his mother and acts as the catalyst for Theodore's challenging coming-of-age journey, whereby he grows from a scared, confused, depressed and grief-stricken boy into a mature and responsible adult. In this first-person account, Theo documents his journey, describing his conclusions, or lack of conclusions, regarding the meaning of life.

In the wreckage of the bomb, Theo meets a dying elderly gentleman, who instructs Theo to take The Goldfinch painting, gives Theo a man's ring, and further instructs Theo to go to Hobart and Blackwell to ring the green bell. This elderly man, named Welty, accompanied a young girl Theo's age to the museum. Once Theo saw the young girl with the red hair, named Pippa, he was smitten, as a thirteen-year-old boy may be. Social workers work with Theo to place him in another home, but Theo mentions his elementary school friend, Andy Barbour, who he would like to go and stay with.

At the Barbours, Theo tries to adjust to life on Park Avenue. In some ways, the Barbours' apartment is a comfortable place to grieve, for example, because of the very low lighting. In other ways, Theo feels as if he is on display with the antique furniture, as Samantha Barbour hosts several charity engagements at her home. Theo has to deal with Kitsey and Toddy, Andy's two younger siblings who resent Theo's presence because he takes their parents' attention away from the youngsters. There is an aura of mystery, of which the details are kept hidden from the Barbour children, over the health of Mr. Barbour. Mr. Barbour is an avid sailing participant, who loves the open seas and skies. During Theo's stay, he visits the shop of Hobart and Blackwell to return the ring to Hobie and sees Pippa once again. He continues to visit the shop. At the end of Theo's stay with the Barbours, Larry Decker, Theo's father, moves Theo to Las Vegas.

In Las Vegas, Theo meets his great friend Boris, who follows his heart much of the time and does not make excuses for who he was born. The two bond through excessive use of drugs, alcohol, petty thievery, and work in the criminal art underground. After Theo's father fails to pay a gambling debt, and Bobo Silver pays a couple of visits to the Decker home to collect on the debt, Theo's father asks Theo if he can get any money out of his college fund. Theo's lawyer tells him that he cannot withdraw the money for anything other than his education. Soon after, Larry Decker dies in a drunk-driving car accident. Theo flees Las Vegas and returns to New York.

Once in New York, Theo asks to stay at Hobie's, to which the lawyer agrees. Theo attends college, but finds he enjoys working in Hobie's antique furniture restoration business. Hobie makes Theo a business partner, only to find that Theo has been selling fraudulent pieces of furniture as the expensive authentic versions. The Goldfinch painting has traveled with Theo from New York, to Las Vegas, and back to New York again, or so Theo thinks. Theo is in a high state of anxiety because a man who calls himself Lucius Reeve is threatening to expose Theo and Hobie for the fraudulent furniture sales. Reeve also thinks Theo has The Goldfinch painting, which he offers to buy from Theo. Theo denies all accusations. When Boris bumps into Theo in New York, Theo is engaged to Kitsey Barbour after the deaths of Mr. Barbour and Andy in a sailing accident. Boris tells Theo that he stole the painting from him. When Theo goes to the storage locker to retrieve the painting, which he thought he had this whole time, he finds Boris's ex-girlfriend's Civics textbook.

Boris wants to make this up to Theo, and he masterminds a scheme for the two of them to go to Amsterdam, where Boris thinks the painting is now located. Theo will act as a rich American buyer of the painting, and reclaim The Goldfinch. Something goes terribly awry, and Theo, in an act of self-defense, shoots a man named Martin, who stepped in at the last minute to steal the painting.

Theo hides in his hotel room in Amsterdam, waiting for Boris to get back to him. Theo says that he feels dead himself; he has committed an ultimate act which cannot be undone. Theo thinks of suicide and of going back to New York, only he cannot because Boris has his passport. One night, Theo's mother comes to him in a dream. Theo is elated, and upon awakening, he decides he will turn himself in. Soon after he makes this decision, Boris arrives at his hotel room, with a satchel full of money. Theo does not want the money, until Boris tells him that the money is legal. Boris masterminded another scheme whereby his organization made a phone call to the art cops. This one phone call regarding the whereabouts of this one painting, The Goldfinch, led to the recovery of many other stolen artworks.

When Theo finally makes it back to New York, he travels the country buying back the fraudulent antique furniture. Theo has grown from a child to a more responsible adult; however, he concludes that some questions may never have answers, no matter how much one searches.