In Spain, young Ferdinand lives with other calves and bulls at Señor Moreno’s “Casa del Toro”, where bulls are trained for the bullfighting ring. Ferdinand is a pacifist, and is bullied by the other calves Valiente, Guapo, and Bones. A matador arrives, and the calves’ fathers fight to impress him. Ferdinand’s father Raf is picked, and Valiente squishes Ferdinand’s favorite flower in retaliation. Raf does not come back from the ring; realizing his father is dead, Ferdinand runs away from Casa del Toro. He winds up on a flower farm owned by Juan and his daughter Nina, who adopt him, much to the annoyance of their dog Paco.
Some years later, Ferdinand has grown into an enormous but still-gentle bull. Juan determines that Ferdinand looks too intimidating to take along to the annual Flower Festival in Ronda, as in previous years. Ferdinand follows them anyway, but is stung by a bee and panics, accidentally destroying the town square. Animal Control officers deem him dangerous, and take him away before Nina and Juan can explain.
The officers decide to give Ferdinand to Casa del Toro, where he meets his old comrades Valiente, Bones, and Guapo, as well as new additions Lupe the goat, Angus the Highland bull, and lab-cloned Galloway Maquina. Ferdinand tries to escape, but is stopped by three German Lipizzan horses, who now keep watch to prevent any more bulls from escaping.
Snooty matador El Primero arrives, needing a bull for his final bullfight before retirement. Moreno puts all the bulls in a ring to fight it out, but Ferdinand refuses to take part, causing a chain of mishaps when he tries to help Guapo recover from a stage-fright-induced faint. El Primero gives Moreno two days to get the bulls into shape. Guapo is sent to the chop house, and Valiente informs a horrified Ferdinand that non-fighters now become meat.
That night, Ferdinand comforts Bones as he grieves for Guapo, making a friend of him. The next day, he fixes Angus’ hair so he can see better, earning another friend. Ferdinand, Bones, and Angus then challenge the horses to a dance off, and Maquina joins in the fun, helping them win. Valiente mocks them for bonding and wasting valuable practice time, causing the other bulls to sadly abandon Ferdinand and return to training.