The show tells the story of Anne Boonchuy, a self-centered 13-year-old who is magically transported to the fictitious world of Amphibia, a rural marshland full of frog-people and dangerous creatures. With the help of an excitable young frog named Sprig Plantar, Anne will transform into a hero and discover the first true friendship of her life.
Season two finds Anne and the Plantars on a quest to unlock the mysteries of the music box as they leave the cozy confines of Wartwood for the distant city of Newtopia. On their journey, they will visit exotic new locations, uncover hidden secrets and experience unexpected reunions as they continue to search for a way to get Anne home.
Amphibia is one of the few non-action two-dimensional animated cartoons to have a human character animated with five fingers. The anthropomorphic amphibians having four fingers makes sense since real-life amphibians have four digits on their hands.
The episode title cards depict a wood carving in darkness lit up with the title superimposed over it. This is an actual wood carving that is photographed and reused every episode.
The show was originally titled Amphibiland but was changed due to sounding too similar to Amphibilands,  the setting of the young adult novel series An Army of Frogs which was adapted into the animated series Kulipari which was released on Netflix from 2016 to 2018. Both series also have Keith David.
On August 22, 2020, creator Matt Braly said that he has plans for the series to feature LGBT characters.