In 1282 Eudokia married in ConstantinopleJohn II Megaskomnenos, Emperor of Trebizond with whom she had two sons, Alexios and Michael. In 1298, after her husband's death and ascension of her son Alexios II, she took the younger son with her and returned to her brother's court at Constantinople.
Andronikos II Palaiologos received his sister well, promising to send her back whenever she wished to her elder son, whose position — such was the official Byzantine version — he did all in his power to consolidate.
Eudokia had become entirely devoted to Trapezuntine interests. She refused a second marriage with King Stefan Uroš II Milutin of Serbia, as she wished to keep her troth to her first consort, and secretly opposed her brother’s plan of marrying Alexios II to a daughter of the high court official Nikephoros Choumnos. She pretended, however, to approve this match, so that, under pretence of making arrangements for her son’s wedding, she might return to Trebizond.
Meanwhile, Alexios II decided for himself to marry Djiadjak Jaqeli, an Iberian princess. His uncle Andronikos II wanted this marriage annulled, so Eudokia, on the pretext of inducing her son to dissolve the marriage, succeeded in returning to Trebizond in 1301, where she advised her son to keep his Iberian wife. Eudokia died in the following year, and was perhaps buried in the church of Saint Gregory.