The TV show didn't follow the books faithfully, the violence was toned down, many aspects of the characters' roles within the Animorphs, the events in the war against the Yeerks were altered, and added plot lines that were not present in the books were added.
- In the books, Rachel acquired the morph of a crocodile but had an allergic reaction to it which caused her to morph out of control and she eventually "burped" the morph out of her, but on the show, they changed it so that Cassie was the one who acquired the crocodile morph and had the allergic reaction which she then "burped" out.
- One big change was how Ax was introduced. In the books, Ax was force to stay on the Andalite Dome ship while his fellow Andalites fought the Yeerks from above Earth, and when the Dome Ship was destroyed, he and the dome ended up at the bottom of the ocean and the Animorphs morphed into dolphins to get to him and escape. In the show, Ax traveled to Earth alone and crash-landed nearby and the Animorphs found him in a old abandon building and to escape from Visser Three and the Controllers, they morphed into butterflies.
- In the books, Tobias morphed into a Red-tailed Hawk, which he became trapped in and then became his true form, but in the show, they used a Harris's Hawk for Tobias instead.
- In the books, Jake could morphed into a Orange Siberian Tiger, but on the show, they changed it so that he would morph into a White Bengal Tiger.
- There were many animals the Animorphs could morph into in the books but some of couldn't be used on the show because they were too dangerous to handle and couldn't be handled in real life. For example, Rachel could morph into a African Elephant and Marco could morph into a gorilla, and the crocodile that was used in the show was smaller, which made it safer to handle than a full-grown one. Also included were sea animals like sharks, whales, and even a giant squid.
- One reasonalbe change was that in the books, when the Animorphs morphed, they lost their clothes, and when they morph back into humans, they end up naked, but they soon learned to morph clothing, unfortunately, it was only skin-tight outfits and nothing else, not even shoes. In the series, however, when they morphed, their clothes disappered, and when they morph back into humans, their clothes reappered on them.
- In the book series, the Animorphs rarely acquired morphs if they did not have a specific use for them. But in the TV series, Cassie encourages this behavior, acquiring whenever they can.
- In the TV series, the Animorphs meet the Ellimist when they are captured in a net by the Yeerks in the forest, as they searched for Ax. Bu in the book series, the Animorphs were infiltrating the Yeerk Pool as cockroaches when they were suddenly swallowed by a Taxxon and about to be digested. Allowing Rachel to notice a human-Controller flying up a dropshaft was the Ellimist's subtle interference, and that allowed the Animorphs to escape the Yeerk Pool once they burst from the Taxxon's stomach. The Ellimist also shows the kids the future so that they may deduce the location of the Kandrona, atop the EGS tower; in the TV series, the point of showing them a Yeerk-controlled future is so that Rachel may bring a knife back to their reality, which allowed them to escape the net. The Animorphs discover the location of the Kandrona by overhearing a telephone conversation between Tom and another Controller regarding the new Kandrona's installation.
- In the book series, Jake uses Cassie's dad's cell phone to call Tom and partially changes his head to wolf to disguise his voice. But in the show, they changed it so that Jake makes his call at Cyberia and Ax uses a voice filter to disguise Jake's voice.
- In the book series, Temrash 114 succumbed to the fugue and squirms out of Jake's ear where he shrivers up and dies, but on the show, they changed it so that the Yeerk just squirms out of Jake's ear and Jake squishes it. The show also has no mention of Crayak.
- In the book series, Drode gave Jake the choice to return to a normal life, to not fight the Yeerks and not have the power to morph. But on the show, they changed it so that the Ellimist was the one who gave Jake the choice, and in the show, Tobias still had his morphing power and was the only Animorph that was fighting the Yeerks.
- Many aliens, characters, and locations didn't appear in the TV show.
- The Kandrona in the TV series, unlike in the books, emited a visible red light ray.
- In the TV series, the Animorphs don't refer to themselves as the Animorphs, but the Yeerks still refer to them as the Andalite bandits.
- In the books, Tobias was the first Animorph to try morphing, by becoming his pet cat Dude, but on the show, they changed it so that it was Jake who morphed first, by becoming his pet dog Homer, which he did, after Tobias morphed.
- In the book series, Elfangor told the Animoprhs that one of them go inside his ship to get the Escafil device and Jake was the one to get it. But in the TV show, Elfangor already had the Escafil device with him.