In December 1984, Haidallah was deposed by Colonel Maaouya Ould Sid'Ahmed Taya, who, while retaining tight military control, relaxed the political climate. Ould Taya moderated Mauritania's previous pro-Algerian stance, and re-established ties with Morocco during the late 1980s. He deepened these ties during the late 1990s and early 2000s as part of Mauritania's drive to attract support from Western states and Western-aligned Arab states. Mauritania has not rescinded its recognition of Polisario's Western Saharan exile government and remains on good terms with Algeria. Its position on the Western Sahara conflict has been, since the 1980s, one of strict neutrality.

Ordinance 83.127, enacted 5 June 1983, launched the process of nationalization of all land not clearly the property of a documented owner, thus abolishing the traditional system of land tenure. Potential nationalization was based on the concept of "dead land", property that has not been developed or on which obvious development cannot be seen. A practical effect was government seizure of traditional communal grazing lands.

In April 1986, the Manifesto of the Oppressed Black Mauritanian (Manifeste du négro-mauritanien opprimé), which documented discrimination against Mauritania's black populations in every sector of public life, was published by the African Liberation Forces of Mauritania (ex-FLAM; Force pour la Liberation Africaine de Mauritanie). In response, in September 1986, 30 to 40 black intellectuals suspected of involvement in the publication of the Manifesto were arrested and subjected to brutal interrogations. They were not allowed visitors until November 1987. In the meantime, the authorities cracked down on black communities, often using mass arrests as a form of intimidation.

In October 1987, the military government allegedly uncovered a tentative coup d'État by a group of black army officers, backed, according to the authorities, by Senegal. Fifty-one officers were arrested and subjected to interrogation and alleged torture. They were accused of "endangering the security of the State by participating in a conspiracy to overthrow the government and to provoke killing and devastation among the inhabitants of the country" and tried following a special summary procedure. Three of the officers arrested in October were sentenced to death; eighteen were sentenced to life imprisonment (including two who died in detention in 1988); nine were sentenced to twenty years; five were sentenced to ten years; three were given five years; six were given five-year suspended sentences with heavy fines; and seven were acquitted. None of those convicted were permitted to appeal.

The discord between conflicting visions of Mauritanian society as either black or Arab, again rose to the surface during the intercommunal violence that broke out in April 1989 (the "1989 Events"), when a Mauritania-Senegal border dispute escalated into violence between the two communities.

In villages of the South, blacks were indiscriminately expelled by security forces, who forced them to cross the Senegalese River to Senegal, taking their identity cards and their belongings. Those who resisted were imprisoned and sometimes executed.

In the larger towns and cities, the authorities targeted black civil servants, employees of private institutions, trade unionists, former political prisoners.

In October 1987, the Government allegedly uncovered a tentative coup d'état by a group of black army officers, backed, according to the authorities, by Senegal. Fifty-one officers were arrested and subjected to interrogation and torture.