In 1253, John III arranged the marriage of Theodora to Michael Palaiologos, who had been steadily rising in distinction due to a combination of familial connections and military abilities.

[3] There is no clear indication that Theodora was crowned empress at this time, but Alice-Mary Talbot notes the historian George Pachymeres contrasts the imperial couple with the young John who wore less impressive regalia.

In September Michael was crowned Emperor a second time in the cathedral of Hagia Sophia; although D. Geanakoplos assumes that Theodora also received a second coronation, this is not expressly stated by Pachymeres.

When Michael pursued a policy of church union at the Second Council of Lyons in 1274, there is evidence showing Theodora originally sympathized with the anti-unionists.

[8] At some point after Michael's death in 1282, Theodora undertook the restoration of Lips monastery (now the Fenari Isa Mosque) which had been founded in the 10th century, and added a convent.

Talbot explains one motivation for her interest in the convent of Lips was to provide a place for her daughters and granddaughters to retire in their old age, per the current custom.

Talbot explains, "Theodora, as dowager empress and matriarch of the family, no doubt was determined to make provision for proper burial for herself and her descendants.

For example, soon after the recovery of Constantinople, she commissioned the monk Arsenios to translate into Greek a work on geometry by the Persian philosopher al-Zanati.