His military record against the Seljuk Turks was not particularly distinguished, but on his return to Constantinople in 1078 he gained the favour of Emperor Nikephoros III Botaneiates, and of Empress Maria of Alania.

During Alexios' reign and until his death, Isaac played an important role in domestic affairs in matters of public order and justice, being called to examine several cases of conspiracy or heretical teachings.

[2] According to his niece, the historian-princess Anna Komnene (Alexiad, 77–78), he was physically similar to his younger brother, the future emperor Alexios, though he was paler and his beard was less bushy.

According to all sources, Isaac was extremely well educated; the Patriarch of Antioch, John the Oxite, records that he was competent in the interpretation of scripture, while Basil of Euchaita credits him with an extensive knowledge of philosophical matters.

[2][7] Shortly after, probably in 1073, he was appointed as domestikos ton scholon of the East,[a] and sent as commander-in-chief (strategos autokrator) to campaign in Anatolia against the Seljuk Turks, who had invaded the area following the Battle of Manzikert in 1071.

[15][16] Once back in the capital, he quickly gained the favour of the new emperor, the elderly Nikephoros III Botaneiates (r. 1078–1081), reportedly due to the latter's fondness for Syrian textiles, which Isaac often gave him as gifts.

Accordingly, Botaneiates often called Isaac to dine at his table, gave him the high title of sebastos and the right to reside in the imperial palace.

[15][16][17] Despite the favour shown to them by Botaneiates, Isaac and Alexios plotted to advance the position of the Komnenos clan by deposing the emperor and seizing the throne.

[18] The brothers found an opportune moment in late January 1081, when the sack of Cyzicus by the Seljuks led to a concentration of troops in Thrace, close to the capital.

[1] Isaac already bore his new title in May/June, when he was charged with leading Empress Maria of Alania to the Mangana Monastery, where she was confined on the insistence of the Doukas clan.

Thus, in the winter of 1081/1082, and without prior warning, Isaac went to the Hagia Sophia, convened the patriarchal synod, and in a forceful speech convinced the clergy to allow the confiscation and melting of gold and silver items to cut coin to pay the troops.

Once again Leo of Chalcedon began to denounce these measures, and in late 1087 Isaac, who once again was left in charge of Constantinople in his brother's absence, exiled him to either Sozopolis or Mesembria on the Black Sea coast of Thrace.

According to Anna Komnene, who gives a detailed account of the proceedings, Isaac himself was not certain of his son's innocence, and maintained a cautious stance until he realized that Alexios himself did not intend to press the matter.

Leo's nephew, Nicholas of Adrianople, in a letter to his uncle, wrote that Isaac denounced those who opposed the confiscations as "worshipers of matter" (ὑλολάτραι), claiming that they accorded to the precious decorations of the icons the same veneration as to the saints depicted on them.

[27] As a result, in late 1094, a church council was held at the Palace of Blachernae that examined the affair, under the direct presidency of Alexios I, with Isaac as one of the three judges, along with the patriarchs of Constantinople and Jerusalem, Nicholas Grammatikos and Symeon II.

[20][30] Isaac also played a leading role in the uncovering of the conspiracy of the four Anemas brothers, which took place sometime between 1097 and 1104 and involved several senior military and civil officials.