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.
The FCC has said Sister Lucy was expelled on the grounds that her "lifestyle was in violation of the proper law" of the congregation. Sister Lucy, however, has said she was actually dismissed because she took a prominent role in the protests against the bishop.
She told the BBC's Yogita Limaye that she was "not at all satisfied" with the Vatican's response. She alleges church officials did not even contact her to get her side of the story.
"I am not going to leave the convent. The lifestyle I lead is as per the rules and regulations," she added.
Although the letter she received from the Vatican says she could "present a new recourse" if she felt that the ruling was "against her lawful rights", she said she had no plans to appeal.
"I am allowed a second appeal but I don't see any point in doing that since they have made up their mind. I will now go to court on behalf of all the people who are being suppressed and facing illegal behaviour from authorities of the congregation," she told the BBC.