Magneton made its proper debut in Clemont's Got a Secret. It served as a patrol for the Gym. After Ash defeated Magnemite with Froakie's help, Magneton appeared and attacked the group with Metal Sound. Serena's Fennekin battled Magneton and attacked with Ember, which Magneton easily dodged by temporarily separating itself into three. Despite having a type-disadvantage, Magneton overpowered Fennekin and Froakie came to the rescue by stopping it with its Frubbles.
After Clemont had his battle with Clembot to determine ownership of the Gym, Magneton cheered along with the group and Clemont's other Pokémon when Clemont was able to reprogram Clembot.
Magneton has been shown to be very loyal, both to Clemont and Clembot, albeit to a fault, as shown when Clembot's orders for it to attack any intruders led to it attacking Clemont, demonstrating that when it is given orders from either of them, it takes those orders very seriously. It was also seen cheering for Clemont when he successfully reprogrammed Clembot. It has the ability to split itself into three separate units, and utilizes this talent to evade oncoming attacks.