The Amanayé were first mentioned in the region that is likely to be their area of origin of this Tupi people: the Pindaré River. There they resisted for several years the efforts for their aldeamento (to be put in villages). But in 1755 they made a deal with Father David Fay, a Jesuit missionary among the Guajajara of the São Francisco do Carará village. Fay "managed to practice the Amanaios and that they come down and settle in a village" together with the Guajajara, their traditional enemies.

Shortly afterwards, part of the group peacefully moved to the Alpercatas River, on the border of Maranhão and Piauí, settling near the village of Santo Antônio. By 1815 just 20 of them remained, mixed with blacks. Other Alpercatas Amanayé continued their migration along the Parnaíba River, reaching Piauí in 1763. There are no records of what happened to them since.

On the second half of the 19th Century, the Amanayé of the Pindaré and Gurupi Rivers were in the area of influence of the Diretorias Parciais (Partial Directorships), where traveler Gustavo Dodt visited them. The Diretorias Parciais were created by an Imperial Regulation in 1845 and were designed to prevent the abuses practiced by the regatões (merchants who plied the Amazon rivers selling merchandise and buying local products); in practice, however, these local administrations increased the Indians' subjection by using them as 'docile' and cheap labor. Because of their chaotic administration, the villages of these Directorships were abolished in 1889.

Forming enclaves in the territory of the Tembé Indians, the Amanayé were, at that time, divided into three villages along the Caju-Apará, one of the rivers that form the Gurupi; considerably smaller than the Tembé, their population was estimated to be between 300 and 400 individuals. There "they have many relations with the civilized population, through the regatões, who come to them in search of copaíba oil, bark, abuta branches and some tar".

Around the same time, other Amanayé are mentioned as being on the Moju River, where they also ran into Tembé Indians who were migrating towards Pará. From then on there is no more information on the Maranhão Amanayé. Settled in the region of the Moju and Capim rivers, these Indians faced mandatory aldeamento, extortions by regatões and conflicts with landowners. They were aldeados in the Anauéra Mission, or São Fidélis, on the Capim River. Because they were considered more 'rebellious', the missionaries separated them from the Tembé and the Turiwara.

In 1873, the Amanayé killed the village missionary, Cândido de Heremence, and a Belgian engineer who happened to be in the area. The retaliations against them led part of the group into hiding near the igarapé Ararandeua, where they avoided contacts with the regional population. According to Nimuendajú, these Amanayé began to identify themselves as Ararandeuara or as Turiwara in order to disguise their identity.

As for the Amanayé who remained in the mission, they stayed where they were but were put under the administration of a Diretoria Parcial de Índios (Partial Directorship of Indians). There, they continued fighting against neighboring peoples. In 1880, the Amanayé killed a group of Tembé and Turiwara, considered the area's 'tame Indians'. This incident led the president of the Province of Pará to give "weapons and ammunitions so that these tame Indians are able to defend themselves from the attacks by the Amanyé". After this, it is thought that the Amanayé totally separated themselves from the Tembé and the Turiwara, migrating to the headwaters of the Capim River. Since the end of the 19th Century, news of the group come only through the notes of the few ethnologists who briefly visited the region and the reports of visits, also brief, by officials from the Serviço Nacional do Índio (National Service for the Indian) - SPI.

Towards the end of the 19th Century, a small band made up of Amanayé and Anambé Indians, survivors of an epidemic that ravaged the Arapari village, was close to the last falls of the Tocantins River. The majority of the group, however, is thought to have remained on the Capim River, where inspector Luiz Horta Barbosa, soon after the creation of SPI (in 1910), made an expedition to. He ran into an Amanayé group led by a mulatto woman called Damásia on the igarapé Ararandeua. Damásia supposedly became the leader of the group still in the end of the 19th Century, and is mentioned as the group's representative well into the 1930s. By then, the Ararandeua Amanayé were about 300, scattered through four villages. It is in this very area that there is supposed to have happened, in 1941, an attack, according to a SPI document: non-pacified 'Amanaja' Indians from the region of the Surubiju and Carandiru rivers reportedly attacked Capim River Indians; according to the Anambé, the strayed Indians were approximately 200, and had already been spotted at the igarapé Pimental, a tributary of the Gurupi River. The documents comment on the need for the creation of an Indigenous Post in the region.

The creation of the Amanayé Reservation, in 1945, was supposedly aimed at this group of 200 'non-pacified' Amanayé, whose remainders constitute, probably, the present Indigenous populations of the Upper Capim. As for Damásia's group, the last information about it dates of 1942 and reported 17 individuals, 'most of them mixed-bloods', led by her son. At the time, those Amanayé mentioned the strayed group of the Garrafão River, a left-margin tributary of the Ararandeua.

Finally, the Amanayé settled on the region of the Moju River identified themselves as Ararandeuara, according to Lange. This traveler published, in 1914, the sole ethnographic description that exists of the Amanayé people. In 1926, Nimuendajú found a local group with the same self-denomination, in the locality of Munduruku. The Cairari River Indians, also visited by Nimuendajú, but in 1943, were identified by him as Amanayé and Turiwara, but may have been in fact an Anambé subgroup.

In the 1950s the Amanayé continued to live along the Candiru-Açu River, inside the reservation. There they were visited by the sertanista (expert on contacting Indians) João E. Carvalho, who at the time was engaged in the SPI's Pacification Front of the Urubu-Kaapor. In 1976 there were at least 10 remaining members of the group scattered through the reservation between the rivers Ararandeua e Surubiju.