When Alexius became emperor in April 1081 he reportedly planned to repudiate Irene and wed Mary, who had been married to the former emperors Michael VII Ducas and Nicephorus III Botaneiates. It was probably fortunate for Alexius that his plan was foiled, for his repudiation of his wife would have incurred the enmity of the powerful Ducas family. Irene was crowned on April 11, 1081, seven days after her husband.

In violation of the rights of John, the eldest son of Alexius and Irene, the empress supported the attempts of her daughter, Anna, to secure the throne for her second husband, Nicephorus Bryennius (Bryennius, Nicephorus). Shortly before his death, the emperor, aware of the intrigues of his wife and daughter, ordered John to proclaim himself emperor. John had himself crowned in the church of Hagia Sophia and then, with his supporters, occupied the heavily fortified palace. Alexius died in August 1118, and Irene, frustrated in her attempts to deprive John of the throne, retired to a monastery that she had previously founded in Constantinople.