The accession of John was contested. As Alexios lay dying in the monastery of the Mangana on 15 August 1118, John, relying on trusted relatives, especially his brother Isaac Komnenos, gained entry into the monastery and obtained the imperial signet ring from his father. He then assembled his armed followers and rode to the Great Palace, gathering the support of the citizenry on the way. The palace guard at first refused to admit John without clear proof of his father's wishes, however, the mob surrounding the new emperor simply forced an entry. In the palace John was acclaimed emperor. Irene, taken by surprise, was unable either to persuade her son to step down, or to induce Nikephoros to contend for the throne.

Alexios died the night following his son's decisive move to take power. John refused to attend his father's funeral, despite the pleas of his mother, because he feared a counter-coup. However, in the space of a few days, his position seemed secure. Within a year of his accession, however, John II uncovered a conspiracy to overthrow him which implicated his mother and sister. Anna's husband Nikephoros had little sympathy with her ambitions, and it was his lack of support which doomed the conspiracy. Anna was stripped of her property, which was offered to the emperor's friend John Axouch. Axouch wisely declined and his influence ensured that Anna's property was eventually returned to her and that John II and his sister became reconciled, at least to a degree. Irene retired to a monastery and Anna seems to have been effectively removed from public life, taking up the less active occupation of historian.