They segue into the episode by asking "Imagine we had the powers" of the animal and then posing while saying "What if?" together, transforming them into animated versions of themselves. The episode then transitions to the animated segment, where the brothers go on expeditions to study animals "living free and in the wild." They usually end up rescuing animals from threats caused by a baby animal's confusion, human influence, or villains such as Zach Varmitech, Gaston Gourmand, Donita Donata and Dabio, and Paisley Paver and Rex. Some episodes aim to change how animals, such as bats and crocodiles, are perceived by showing how they are an important part of their habitat.

The Kratt brothers are supported by Aviva Corcovado, a biomechanical engineer who invented "creature power suits", which allow humans to mimic the abilities of animals, and other equipment to aid the brothers in studying animals and defeating villains; Koki, a mechanical engineer and computer expert who maintains their flying turtle ship, the Tortuga; and Jimmy Z, the Tortuga's pilot, who operates the teleporter to send equipment to the brothers and helps Aviva test inventions. Along the way, the team and viewers learn about animals as the team uses creature powers to right wrongs or get out of the situations they find themselves in. They also occasionally enlist the help of the Wild Kratts Kids, children who help the Wild Kratts from their homes in any way they can, whether it be moving animals, helping to rebuild habitats, or providing local knowledge about the animal in question.

At the end of each episode, the animated segment transitions back to the live-action segment, with the Kratt brothers reiterating the animal's powers and, before the end credits, signing off by saying "Keep on creature adventuring! We'll see you on the creature trail!"