Isaac Kontostephanos first appears in 1080, during the imperial campaign against the rebel Nikephoros Melissenos. During this expedition, he fell off his horse and was nearly captured by Melissenos’s Turkish allies, but was saved by George Palaiologos. He is next attested, holding the rank of protonobelissimos, at the 1094 synod of Blachernae.
By 1105, Kontostephanos had become a senior admiral (doux) in the Byzantine fleet. With the anticipated Norman invasion of Bohemond drawing near, Emperor Alexios I Komnenos (r. 1081–1118) named Kontostephanos megas doux (commander-in-chief of the imperial fleet) in succession to Landulf, and sent him to Dyrrhachium to intercept the Normans. On his own initiative, however, Kontostephanos resolved to attack the city of Otranto in Italy, which was defended by Emma of Hauteville. Although his forces could have taken the city by storm, Kontostephanos allowed himself to be involved in negotiations with Emma, which she dragged on until Norman reinforcements arrived. Defeated in battle by the newly arrived Norman troops, Kontostephanos and his fleet were forced to withdraw to the Albanian coast. Making Aulon his base, he began patrolling the Strait of Otranto. At the news that Bohemond’s army was preparing to cross the sea, however, most of the army panicked and fled to Himara, while Kontostephanos was unable to reimpose order.
After Bohemond’s successful landing, the emperor charged Kontostephanos with intercepting the Norman supply convoys, but here too he failed. After receiving letters from Landulf detailing Kontostephanos’s incompetence, Alexios finally dismissed him in summer 1108 and replaced him with Marianos Maurokatakalon.