With the Clone Saga happening in the mid 1990's, it was only natural that Ben would make it into another medium. Marvel produced some of it's best animated shows during the 90's, with X-Men, Fantastic Four and Spider-Man cartoons leading the way in terms of popularity and success. Ben made a small cameo in the Fantastic Four cartoon in his Scarlet Spider costume. In a scene from the episode "Nightmare in Green," while Johnny Storm and Rick Jones zip around on a Fantastic Flyer, Ben can be seen for a few moments hanging on a building.
Ben also appeared in a significant role in the last two episodes of the Spider-Man Animated Series entitled "I Really, Really Hate Clones" and "Farewell Spider-Man." The Spider-Man of the Animated Series universe is summoned by the Beyonder and Madame Web to stop Spider-Carnage from destroying the entire universe in a reality which more closely resembled the 616 Universe of the comics. Ben is Peter's clone, however he is unsure who is the real deal and who is the clone. There are a few moments from the comics which are shown in the episode when Ben explains what has happened to cause Spider-Carnage to threaten the destruction of everything. In this reality, Aunt May dies, as she did in Amazing Spider-Man 400, and after Dr. Connors (replacing Seward Trainer) tells Ben that he may be the real Peter Parker, not the clone, Peter goes a little nuts on Ben. While Ben was trying to stop the Kingpin during a theft, Peter interrupts and attacks Ben. The time-dilation accelerator (which Kingpin was trying to steal) is activated and the Carnage symbiote comes through from another dimension, attracted to Peter because of his rage and hatred. The two become Spider-Carnage, who appears as he did in the Comics, even with Ben's spider-suit design. Spider-Man, Ben and Spider-Men from other dimensions help defeat Spider-Carnage who sacrifices his own life after speaking to Uncle Ben, who was still alive in the dimension where the final battle takes place (the universe where Peter is rich, his identity is public and he is engaged to Gwen Stacy.) Miles Warren is also shown in this episode as being the one who cloned Peter to make Ben, as well as the clone escaping from his birthing tube. It also shows Ben cutting and dying his hair blonde, however still wearing the Scarlet Spider outfit, which is a departure from the comics, as he did not change his appearance until he became Spider-Man.