On her retirement from the court, she served as a member of the National Human Rights Commission and later as the Governor of the Indian state of Tamil Nadu from 1997 to 2001.

[2][15] Appointing her as the Governor of Tamil Nadu and Justice Sukhdev Singh Kang, former Chief Justice of Jammu and Kashmir High Court, as Governor of Kerala, the then President of India, Shankar Dayal Sharma said "Their experience of and insights into the working of the Constitution and the laws comprise valuable assets.

"[16] As the Governor of the state, she rejected the mercy petitions filed by the four condemned prisoners in the Rajiv Gandhi assassination case.

[17] Beevi was embroiled in controversy when she gave a clean chit to the law and order situation in Tamil Nadu that prompted the ire of the Central government.

[18] Later she left her office as Governor of the state under controversial circumstances of her accepting Jayalalithaa's assembly majority after the elections[19] and over the arrest of Karunanidhi,[20] who pitched for her appointment four years ago.

There were a few Public Interest Litigations (PIL) filed in the Supreme Court questioning the validity of her appointment as the Chief Minister of Tamil Nadu.

[25][26] Fathima Beevi submitted her resignation after the Union Cabinet decided to recommend to the President to recall the Governor for having failed to discharge her constitutional obligation.

Therefore, the Governor, having due regard to the Constitution and the laws, must decline to exercise the discretion in appointing as Chief Minister a non-member who was not qualified to become a member of the legislature.

Manoharan, had decided to quit his office in the wake of the Chancellor allegedly withholding her approval to the Syndicate's decision to establish a new department for contemporary Tamil literature.

[31] The left parties also discussed the nomination of the prospects of Fathima Beevi as the President of India, during which the NDA Government proposed the name of Dr. A P J Abdul Kalam.