Magmortar debuted in Lost Leader Strategy! as a Magmar where it appeared in a flashback. Reggie explained to Ash that it easily defeated Maylene's Steel-type Lucario with its Fire Spin and Fire Punch attacks, thus earning him the Cobble Badge.
It made its physical debut in Aiding the Enemy!, resting with Paul's other Pokémon.
In A Pyramiding Rage!, Magmar was the first Pokémon chosen by Paul during his match against Pyramid King Brandon. He quickly recalled it after he saw Brandon chose Regirock to battle it. He sent it out again to battle Registeel. Registeel was able to shrug off Flamethrower with little difficulty and struck with Iron Head, not causing much damage but Magmar flinched and couldn't use Will-O-Wisp. Paul recalled Magmar but after all of Paul's other Pokémon were defeated, Paul sent out Magmar to battle Regirock again, who absorbed Flamethrower and took Magmar out with Shock Wave.
In Pedal to the Mettle!, Magmar was revealed to have evolved into Magmortar when Paul chose it as his fifth Pokémon to battle Ash's Pikachu. They began the battle in Evolving Strategies!, where Pikachu got badly burned because of Magmortar's Flame Body. Magmortar's powerful Flamethrower blocked Pikachu's Thunderbolt, and it then cleverly used Rock Tomb to damage Pikachu during his Volt Tackle. Magmortar used Smog in an attempt to choke Pikachu but this was blocked by Counter Shield. However, Pikachu's attempt to follow up with Iron Tail did not cause nearly enough damage to Magmortar, and Ash recalled him for Buizel.
Despite the type disadvantage, Magmortar was able to hold its own, managing to carry on after a direct hit from Aqua Jet. It then used a wall of Rock Tombs to block Water Pulse, which turned out to be a distraction; while Buizel blasted through easily, Magmortar had vanished. It was revealed to have jumped into the air, landing a hit with Smog and poisoning Buizel. While Buizel choked, Paul recalled Magmortar. It wasn't used for the rest of the battle, but the burn it inflicted on Pikachu continued to affect him during a later battle against Ursaring.
In Casting a Paul on Barry!, Magmortar was used in the battle against Barry's Skarmory and it won with a single Flamethrower. Then, Magmortar fought against Barry's Empoleon, where it was shown to be strong enough to withstand Empoleon's Hydro Cannon. It was then recalled by Paul, much to Barry's disappointment.