Alvin, Simon, and Theodore, along with the Chipettes – Brittany, Jeanette, and Eleanor – have moved to a new house and set up a surprise birthday bash for Dave Seville that also serves as a good luck party for the Chipettes, who are scheduled to be guest judges on American Idol. Alvin invites and hires many people and celebrities, much to Simon's dismay. Though dissatisfied, Dave agrees to take them mini-golfing, where the Chipmunks meet Samantha, who Dave has been dating for the past months. While the Chipmunks like Samantha, her son Miles physically torments the trio. Later, the Chipmunks find an engagement ring in a bag Dave brought home and believe that he is going to propose to Samantha. Realizing in horror that Dave and Samantha getting married would make Miles their stepbrother, they unsuccessfully try to steal the ring. Dave has to produce a record for rising pop artist Ashley Grey in Miami, and decides to bring Samantha along with him. The Chipmunks and Miles are staying together, but they agree to head to Miami to sabotage the supposed marriage proposal. The Chipmunks drug three squirrels and dress them up in their clothes from stuffed toys to fool their next door neighbor Ms. Price, who was asked to peek in on them. They travel on a plane, but Theodore lets out a monkey, which then lets out several animals, leading to an emergency landing in Austin, Texas, and frustrates unscrupulous Air Marshal James Suggs, who hates the Chipmunks because of having been dumped by his girlfriend on Christmas for being a fan at the time, effectively eliminating his shot of becoming an FBI agent. Suggs puts the Chipmunks on the No-Fly List as revenge.
The Chipmunks perform at a bar, but are caught by Suggs. Alvin starts a bar fight so they can escape. They jump into a cab, but the driver ejects them for not having money. Resting against an old tree, Miles reveals that his father left him when he was young, causing the four to bond and see each other differently. They raise money busking to take a bus to New Orleans and perform at a Mardi Gras parade, which draws Dave's attention as it is broadcast on live television. The parade allows the Chipmunks to cause Suggs, who has followed them, to get drunk on moonshine. Dave and Samantha find Miles and the Chipmunks at Louis Armstrong New Orleans International Airport and punish them for sneaking out and not responding to numerous missed calls and texts from Dave. With the Chipmunks now on the No-Fly List, Dave has to drive them.
When they arrive in Miami, Alvin reveals that he stole the ring from the container, thus sabotaging the proposal. However, since Miles has grown to care about the Chipmunks during their trip, he is upset that they are celebrating over this. Crossing the street with his headphones on, he is nearly hit by a car, but the Chipmunks swing Theodore, pushing Miles out of the way, saving his life, making Theodore get hit instead, but he wakes up a moment later. They agree to give the ring back.
During the dinner, Suggs catches up with the Chipmunks, but they trap him in an elevator. Miles and the Chipmunks return the ring to Dave, saying that they accept Samantha and Miles into the family, but Dave reveals the ring belonged to his friend Barry, who was proposing to his girlfriend, Alice. As one final apology, they try making it up to Dave by singing a new song to him at the launch party with the help of the Chipettes, Ashley and Miles. They also return the ring to Barry, who reattempts his proposal to Alice, and this time, Alice accepts. Having forgiven them, Dave officially adopts the Chipmunks as his sons, but finds about the squirrels which have destroyed the house, much to his anger. Meanwhile, Suggs is freed from the elevator and decides to relax by the pool, only for security guards to carry him out as he's not a hotel guest.