Sister Lucy Kalappura said she was disappointed by a Vatican decision to reject her appeal against her dismissal from the Franciscan Clarist Congregation (FCC) in Kerala state.
She said she would not leave the convent and now plans to go to court.
Sister Lucy took part in protests against Bishop Franco Mulakkal in 2018.
He was later arrested over allegations he repeatedly raped a nun between 2014 and 2016. The bishop denies all the charges against him.