In 1962, brothers Bob and Horatio Huntington run a traveling circus together, doing well in spite of their vastly different personalities. After a show, the circus’ resident gypsy fortuneteller, Esmerelda presents her beautiful niece, Talia, to her employers, asking them to give her a job. Bob and Horatio are both immediately smitten with the lovely girl, but her affections are solely for Bob. When the pair announce their plans to marry, Horatio becomes furious, and delivers an ultimatum to his younger brother to choose either Talia or himself. Bob marries Talia, and Esmerelda gives them a mysterious box as a wedding gift, which allows them open a new circus; Buffalo Bob’s Rootin’ Tootin’ Animal Circus, known for animals performing amazing, seemingly impossible, feats.
Years later, Bob’s nephew Owen marries a girl named Zoe at the circus. Upon initial excitement however, Owen soon discovers he now has to work as a taste tester for Zoe’s father Mr. Woodley at his dog biscuit factory. Meanwhile, Horatio, whose luck has taken a serious downturn since his break with Bob, sneaks into Bob and Talia’s trailer, trying to find the secret to the magic animals, and accidentally starts a fire which apparently kills Bob and Talia. Their funeral is attended by Owen, Zoe, and their daughter Mackenzie. Horatio makes an unexpected visit, and announces that he’ll be taking over the circus. He and his henchmen start a fight, causing the Huntingtons to flee.
Before they leave, circus pets Old Blue the bloodhound and Zena the cat give the Huntingtons the mysterious box, they later discover it holds animal cracker cookies. Owen eats one and turns into a hamster. The Huntingtons return to the circus to figure out how this happened. They learn from clown Chesterfield that the animal crackers will turn the user into the animal they eat, but it contains only one human cookie to change them back. Later, he tells them they inherited the circus. Zoe is excited, but Owen, determined to please Mr. Woodley, decides to continue his job. Zoe restores the circus while Owen stays at the dog biscuit factory. Mr. Woodley, frustrated that Zoe quit her job, begins to consider Brock, an egotistical saboteur, as her replacement.
Buffalo Bob’s Rootin’ Tootin’ Animal Circus reopens, but is a disaster, upon the discovery of no animals. Owen reluctantly decides to eat the animal crackers and performs stunts as an animal. By the end of the day, Owen grows to like it, and decides to quit his job. As his finishes packing up though, Brock unwittingly eats one of the cookies and turns into a mandrill. To catch up with him, Owen turns into a lion, but Brock gets captured by Horatio’s henchman Mario Zucchini who also steals cookie crumbs. Owen soon discovers he lost the human cookie, and will remain an animal forever. He attempts to adapt to life as a certain animal, but has little success. Binkley, an employee of Mr. Woodley who’s trying to create a new type of dog biscuit, discovers the animal crackers and persuades Mr. Woodley to attend the circus.
At one performance, Horatio offers Owen his human cookie for the circus. Owen however, refuses, thinking remaining an animal will at least keep his family together, but he is forced into the deal by Horatio’s henchmen, who are now mutated animals consumed from the cookie crumbs. The circus performers fight the henchmen. Horatio eats some crumbs and turns into a chimera. He is confronted by Old Blue and Zena who reveal themselves as Bob and Talia, alive but forever trapped in animal form due to the destruction of their human cookies in the fire. They ask Horatio to redeem himself, but he refuses. Horatio flies up, grasping them. Owen, Zoe, and Mackenzie, and the other circus performers work together to save Bob and Talia. Upon capturing Horatio, Owen turns Horatio into a hamster as punishment. Mr. Woodley reevaluates his views on the circus, and with Binkley, decides to create a new circus souvenir using her failed experiments. Owen and Zoe now work happily at the circus, with Owen debuting as a dragon.