In 1998, a report on the still-extant and widespread[3] practice of slavery in Mauritania aired on French television, she and the organization's then president, Cheikh Saad Bouh Kamara, were arrested without warrant.

In 1998, she was sentenced to another prison term of thirteen months for belonging to an unapproved union, yet under the pressure of an international campaign she was pardoned by the country's President.

[5] In 2013, Mbaye joined a three-person UN commission of inquiry in the Central African Republic with Bernard Muna and Philip Alston.

This commission worked in a hostile and violent atmosphere and in a constrained manner, but in 2015 released a final report to the Security Council accusing all belligerent parties in the CAR Civil War of crimes against humanity.

[9] On March 28, 2016, John Kerry, as Secretary of State, recognized Fatimata Mbaye during the 2016 International Women of Courage Awards for her contributions to the legal protection of human rights in Mauritania and her commitment to human dignity, stating: Fatimata M'Baye has long been a voice of reason and of tolerance in a country plagued by ethnic tensions.