After Alexios gained power, Isaac proved one of his most loyal, steadfast and enthusiastic supporters.
Alexios in turn rewarded him by awarding him with the new title of sebastokrator which marked him as a near-equal; in the words of Anna Komnene, an "emperor without the purple".
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.

According to the historian Paul Gautier, Alexios appears to have entrusted his brother with the role of "grand inquisitor and guardian of public order".
As such, Isaac headed a special tribunal, and was charged by Alexios with a number of delicate assignments.
Thus, when Alexios left for the Dyrrhachium campaign against the Normans in autumn 1081, Isaac was left in charge of keeping order in Constantinople.
During the campaign, Alexios was constantly in need of money to pay his troops.
A first appeal for financial aid was met by the Komnenoi themselves, as well as their relatives and supporters, but when a second appeal came soon after, Isaac and his mother, who had been left in charge of the government, were at an impasse.
After long deliberation, they decided to turn to the treasures of the Church—following a precedent set by previous emperors all the way back to Heraclius (r. 610–641).
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.
Only a single member of the synod, the deacon John Metaxas, opposed the move, and even went as far as ridiculing Isaac, but once the confiscation began, Leo, the Metropolitan of Chalcedon, who had not been present at the synod, started to publicly denounce the decision as well as Isaac, its chief instigator.
This led to Leo's trial and dismissal by a mixed court composed of senators and senior clergymen in January 1086.

Because of his extensive education, according to Anna Komnene, Isaac was placed in charge of the inquest against the philosopher John Italos in February 1082.
Finding him guilty of unorthodox teachings, Isaac sent Italos before an ecclesiastical tribunal.
In 1083, he donated precious sacral vestments to the Monastery of Petritzos, founded by the general Gregory Pakourianos.
In 1087, on account of the Pecheneg raids into the Balkans, the confiscation of ecclesiastical treasure was repeated.
According to John the Oxite, some recalcitrant monks who tried to hide precious vessels were even whipped and imprisoned.
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.

In 1092/1094, his son John Komnenos, recently named doux of Dyrrhachium, was accused by Archbishop Theophylact of Ohrid of plotting against Alexios.
A trial was held in front of the emperor at Philippopolis, to where Isaac went in haste.
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.
Then he intervened forcefully in his son's defence, and even quarreled with his younger brother Adrianos, whom he accused of slander.

In the meantime, the affair of Leo of Chalcedon had flared up again.
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.
Leo of Chalcedon responded to his nephew with a long theological defence of his positions, which caused great uproar.
To defend himself from Leo's criticism, Isaac set about compiling a corpus of patristic
After Alexios gained power, Isaac proved one of his most loyal, steadfast and enthusiastic supporters. Alexios in turn rewarded him by awarding him with the new title of sebastokrator which marked him as a near-equal; in the words of Anna Komnene, an "emperor without the purple". 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.
According to the historian Paul Gautier, Alexios appears to have entrusted his brother with the role of "grand inquisitor and guardian of public order". As such, Isaac headed a special tribunal, and was charged by Alexios with a number of delicate assignments. Thus, when Alexios left for the Dyrrhachium campaign against the Normans in autumn 1081, Isaac was left in charge of keeping order in Constantinople. During the campaign, Alexios was constantly in need of money to pay his troops. A first appeal for financial aid was met by the Komnenoi themselves, as well as their relatives and supporters, but when a second appeal came soon after, Isaac and his mother, who had been left in charge of the government, were at an impasse. After long deliberation, they decided to turn to the treasures of the Church—following a precedent set by previous emperors all the way back to Heraclius (r. 610–641). 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. Only a single member of the synod, the deacon John Metaxas, opposed the move, and even went as far as ridiculing Isaac, but once the confiscation began, Leo, the Metropolitan of Chalcedon, who had not been present at the synod, started to publicly denounce the decision as well as Isaac, its chief instigator. This led to Leo's trial and dismissal by a mixed court composed of senators and senior clergymen in January 1086.
Because of his extensive education, according to Anna Komnene, Isaac was placed in charge of the inquest against the philosopher John Italos in February 1082. Finding him guilty of unorthodox teachings, Isaac sent Italos before an ecclesiastical tribunal. In 1083, he donated precious sacral vestments to the Monastery of Petritzos, founded by the general Gregory Pakourianos. In 1087, on account of the Pecheneg raids into the Balkans, the confiscation of ecclesiastical treasure was repeated. According to John the Oxite, some recalcitrant monks who tried to hide precious vessels were even whipped and imprisoned. 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.
In 1092/1094, his son John Komnenos, recently named doux of Dyrrhachium, was accused by Archbishop Theophylact of Ohrid of plotting against Alexios. A trial was held in front of the emperor at Philippopolis, to where Isaac went in haste. 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. Then he intervened forcefully in his son's defence, and even quarreled with his younger brother Adrianos, whom he accused of slander.
In the meantime, the affair of Leo of Chalcedon had flared up again. 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. Leo of Chalcedon responded to his nephew with a long theological defence of his positions, which caused great uproar. To defend himself from Leo's criticism, Isaac set about compiling a corpus of patristic 
Isaac Komnenos (brother of Alexios I)