Pachymeres records her staying in Nicaea through the reigns of both Theodore II (1254–1258) and her step-grandson John IV Laskaris (1259–1261).

Alice Gardner suggested that she was still politically useful as a hostage against the remaining members of the House of Hohenstaufen, particularly her brother Manfred of Sicily.

According to Pachymeres, around this time Michael fell in love with Anna and attempted to marry her, but the widowed Empress rejected him.

Deno Geanakoplos points out "what militates against Pachymeres' statement, however, is the question why Michael, merely for love of Anna, would be willing to risk almost certain excommunication by the Patriarch Arsenios without the gaining of an important political benefit."

She remained for some time at the court of King James I of Aragon, but eventually retired as a nun to a monastery in Valencia, where she died.