In the second season, Kipo learns she was experimented on with mute DNA by her parents before her birth, turning her into a half-human, half-jaguar hybrid, and that her mother Song, previously thought to be deceased, is actually the mega monkey who destroyed her burrow, mutated as a side effect from her pregnancy and mind-controlled with Scarlemagne's pheromones by Dr. Emilia, her parents' former employer who now leads a resistance group against mutes.

She also discovers that Scarlemagne was originally an ordinary mandrill named Hugo whom Kipo's parents turned sentient and secretly raised as their son, but grew to hate them after they were forced to abandon him.

Kipo frees Song from her mind control and defeats Scarlemagne, while Emilia plots to revert mutes back into normal animals.

Mod Frogs Timbercats Newton Wolves Umlaut Snakes Humming Bombers Scooter Skunks Fitness Racoons Other Mutes Humans Kipo and the Age of Wonderbeasts was created by Radford Sechrist, previously a storyboard artist for Dan Vs. and later director on the Voltron: Legendary Defender.

[30] At io9, Beth Elderkin described Kipo as a "must-watch", writing that it joined the likes of She-Ra and the Princesses of Power, Gravity Falls and Steven Universe as a series with a broad appeal to many age groups, and highlighting its music and art design.

[9] At Collider, Dave Trumbore noted Kipo's similarity to other recent female-led animated portal fantasy series such as Amphibia and The Owl House, and described it as a "classic in the making" that drew on cultural touchstones such as Fallout, The Warriors, The Island of Doctor Moreau, Planet of the Apes and Alice in Wonderland.

[31] NPR argued that the series is colorful and funny, with its diversity allowing it comment on sexuality, race, and class, combining the world-building in Avatar: The Last Airbender and the inclusivity, and heart, of a show like Steven Universe.

[33] Writing for Polygon, Petrana Radulovic appreciated that beneath a standard fantasy exploration quest, the series is a "vibrant mosaic, with a unique world, multidimensional character relationships, and a deeper underlying plot" about the tensions between mutes and humans.

[34] She also noted that Benson was the first character to have an explicit coming out as gay in an all-ages animation series, and that the understated manner of the scene, in episode 6, made it all the more noteworthy.

[35] Charles Pulliam-Moore at io9 likewise wrote that the series's "casual queerness is fantastic" because Benson's orientation is not treated as a plot point to complicate Kipo's feelings for him, but, "with a distinct matter-of-factness", as just one aspect of his character.

[36] Dave Trumbore of Collider noted that the show explores "burgeoning same-sex relationships in a positive manner," referring to the relations between Benson and Troy.

"[42] Shamus Kelley of Den of Geek praised the "charmingly cute romance" between Benson and Troy and said they were delighted both were still "together in the five-year time skip.

"[44] In June 2020, Bill Wolkoff, co-screenwriter of Kipo and the Age of Wonderbeasts, said that they were lucky and glad the studio empowered this, wanting to have a "young, 16-ish year old kid" who was gay and was not ashamed of it.

In the interview, Wolkoff said that they did not face roadblocks in presenting Benson and Troy, crediting creators like ND Stevenson, Rebecca Sugar, and others for fighting "difficult battles before Kipo came along.