Although the real Unicron did not make any appearances in 1996's CGI animated series, Beast Wars, his legend held strong. Starscream's ghost spun a lie that claimed Unicron had destroyed him (Unicron's planet mode was seen inStarscream's fabricated flashback), and when the mysterious alien race known as the Vok directly communicated withMaximal leader Optimus Primal, they searched his mind for an image that he would fear and respect, found Unicron and took the form of his head. Later, in Season 3 of Beast Wars, it was revealed that Tarantulas had attempted to destroy both Autobots and Decepticons in the Ark, as he and the Tripredacus Council were descended from a different lineage than Autobot or Decepticon, and would hence inherit Cybertron all to themselves. Although never directly stated, it is implied that the ancestor of Tarantulas and the Council is in fact Unicron; Megatron refers to Tarantulas as "Unicron's spawn" in theBeast Wars episode "Nemesis Part 1".
In Episode 16 of Beast Machines, Rattrap called Megatron's floating head a tribute to Unicron.
Conversely, Unicron played a large role in the two Japanese-exclusive animated Beast Wars series, Beast Wars II andBeast Wars Neo. Following the events of The Transformers: The Movie and Unicron's demise, the Angolmois energy that gave Unicron life was left sealed within planet Gaia (a future version of Earth). When the war on this planet between the forces of Maximal leader Lio Convoy and Predacon leader Galvatron (a different individual bearing the same name as Unicron's original creation) culminated in the explosion of Galvatron's Nemesis battle fortress, the resultant energy surge revived Unicron's consciousness. Seeking to complete his resurrection, he created the Blendtrons to gather the Angolmois Capsules his life-energy was now sealed in, and then proceeded to possess the lifeless body of Galvatron as a temporary host. After gathering the capsules, Unicron attempted to make Cybertron his new body, but was finally defeated by Maximal commander Big Convoy and his Matrix Cannon.
As with his original incarnation, there was a failed attempt to make Unicron into a toy for the Beast Wars Neo line, and although regarded as quite impressive, the prototype - which, notably, does not resemble Unicron from the Beast Wars Neoseries at all - did not make it into the production.