Alexios Palaiologos is instrumental in the suppression of the attempted coup by John Komnenos the Fat in July 1201.

After the rebels had seized control of most of the Great Palace, Alexios is sent by the emperor with troops and boats from the Blachernae to the eastern shore of the city.

Here they meet up with the Great Palace's guard, and clear the palace and the Hippodrome of the supporters of the usurper, who is caught and beheaded.

Alexios Mourtzouphlos is likely put in prison for his role in this affair (he is known to have been in prison in 1203), and the two Komnenos brothers, Alexios and David, seem to have fled the capital immediately after the coup's failure.

Alexios is injured in February 1201 or 1202 when the imperial tent collapses during an earthquake, but in the same summer he leads the campaign that subdues the rebellion of governor John Spyridonakes in eastern Macedonia, forcing the latter to flee to Bulgaria.