Kowalski has been in all three Madagascar movies and also in the specials A Christmas Caper and Merry Madagascar. In the first movie, he plays a small role and is only seen briefly at the zoo, then at the Grand Central Station where he and the other animals were tranquilized, and after reawakening the team seized control of the cargo ship to steer it to Antarctica. When the penguins were in the cargo ship, he was navigating for the team, yet he did not get what the map's navigation points were, which is strange for someone like Kowalski. At the end, he is shown on beach chairs with the other three in Madagascar because Antarctica wasn't that great in their opinion.

In the second movie, he is steering the plane in the cockpit with the other three Penguins, and high fives the other three when they manage to land (although not so well) the plane, in fact half-destroying it. He is shown to be shocked, along with the others, when blackmailing pictures of Skipper kissing the bobble-head Lola are shown by the monkeys. Afterwards, he is shown again at Skipper and Lola's wedding.

In Madagascar 3, Kowalski becomes even more like his spin-off character - he invents a Warp Drive for the Super Plane (later revealed to be part of Alex' dream) and upgrades an SUV with a nuclear reactor for additional speed. When it crashes, becoming utterly destroyed, his genius helps to upgrade the circus into a fantastic lights and music show. Along with the other Penguins, he helps to fight off DuBois.

In A Christmas Caper, he is organizing the HQ for Christmas, and follows Skipper and Rico when they go and find Private. In Merry Madagascar, he is hostile towards the reindeer, like Skipper and Rico, although Private falls for Cupid, a young female reindeer. He then flies Santa's sled with the other three after being covered in the magical dust which lets the reindeer fly. After crash-landing similarly to in Madagascar 2, he still high-fives the others and Skipper remarks "Whoever said penguins couldn't fly?!?", and says a similar line in Madagascar 2 after they emerge from the wreckage of the plane. Afterwards, he returns to Madagascar with Alex, Marty, Gloria, Melman, Private, Skipper and Rico although they all wanted to stay in New York.