Sometime before the XY series, Clemont owned a Magnemite and lent it to Clembot while he and Bonnie were out of the Lumiose Gym.
Magnemite made its official debut in Clemont's Got a Secret when Ash and his friends snuck in the Lumiose Gym. It served as a patrol for the Lumiose Gym while Clembot was in control of it. After Clemont greeted Magnemite upon his return, it was initially happy but then remembered its orders and attacked him with Thunder Shock. It continued attacking until Froakie's Frubbles put a stop to it. Magnemite was then seen along with the other Pokémon cheering for Clemont after defeating Clembot.
In A Fork in the Road! A Parting of the Ways!, Magnemite was added back into Clemont's active party in preparation for his upcoming Gym battle with Ash.
After Clemont's Gym Battle with Ash in The Moment of Lumiose Truth, Magnemite was left back with Clembot.
Magnemite reappeared in XY137, where it was the first Pokémon used by Clembot in a Gym battle with a Trainer named Alva. It started the battle with Electro Ball, but was stunned by Vivillon's Flash-Quiver Dance combo. After being put to sleep with Sleep Powder, Magnemite was quickly defeated by an Energy Ball.
