Alberto is first seen in a cage at Rob's lab. After Ratso makes a rude comment about Maisie and her kittens, Alberto angrily demands Ratso to knock it off. When Ratso makes a rude statement about Alberto as well, the Chihuahua retorts, "You stop that, you dirty rat, you!" Ratso then contradicts Alberto by stating that rats are not dirty.
Alberto is later present during the "Remember That Day" sequence and recalls the time when Rob (the Master) first found him after he attempted to cross a street while dodging oncoming traffic, but broke his hind leg against a lamppost in the process. Presumably after this, the Master bandaged his broken leg. At the end of the song, Alberto licks a photo with the Master's face on it, indicating how much he loves him.
Alberto is shown to sleep with a stuffed teddy bear that also has one of its legs bandaged. He loves his teddy bear almost as much as he loves the Master who mended his hind leg. Sometime later, Alberto and the other animals learn that Mack plans to ship them to Tartarus Laboratories to be used as test subjects, and Alberto expresses how scared he is to go there, even whimpering in fear.
Ratso later leads Toaster and company to a recent disturbance that was coming from the basement. However, Mack shows up shortly after and prepares to ship the animals, but is stopped by Kirby (who was unable to fit inside the vent and was then given the duty to protect the animals). Alberto watches with delight as Kirby chases Mack around the lab, but the latter eventually manages to lock Kirby in a closet.
When Alberto and the other animals are eventually shipped by Mack, Toaster and friends chase down the truck. At one point, the truck goes over a few bumps in the road, shattering Murgatroid's glass tank. When he complains, Alberto says, "Why don't you do something about it?" after which Murgatroid takes the Chihuahua's advice and does so. When Toaster and the gang manage to catch up with the truck, Ratso asks if everyone is okay, and Alberto replies, "Muy bien. Gracias."
Back at the Master's lab, Alberto's hind leg is shown to have healed, and Chris reveals that Alberto has been adopted by the Dean family and given a new home. The Master then pets Alberto on the head, much to the Chihuahua's pleasure.
Alberto is last seen residing in his new owner's home during the "Hang in There, Kid" sequence and hugging his teddy bear that no longer has a bandage on its leg. He also appears briefly on Wittgenstein's computer screen with all the other protagonists of the film.