After the establishment of Islam, its rapid expansion and conquests displaced traditional African religions either by conversion or conquest. Traditional African religions have influenced Islam in Africa, and Islam is considered as having more commonality with traditional African religions, but conflict has occurred, especially due to Islam's monotheistic stance and the rise of Muslim reformers such as Askia.
Traditional African religions are tolerant of other gods, which allows general co-existence for multiple religions. This has been regarded by some authors to be another reason behind the rise of other religions in Africa. Most followers of traditional religions accommodated Islam during the start of its spread in Africa, but in West Africa, it was not until the coming of colonialism that Islam gained mass appeal, transforming even groups with historical animosity towards Islamic domination into Muslim communities.
In many instances, conflicting groups chose to align with Muslim armies against other African communities.
The relationship of Islam and traditional African religions was far from hostile but more defined by accommodation and co-existence. The tradition of jihad remained a minor theme.
In the Songhai Empire, the ruler Sonni Baru held or syncretised aspects of the African traditional religions and was challenged by Askia because he was not seen as a faithful Muslim. Askia would later wage wars against those who were politically non-aligned Muslims and non-Muslims.
In the Swahili coast, Muslims were not interested in preaching, colonization, or jihad. It was not until the 18th century that Islam spread into the interior. Molefi Asante notes that:
The religion of Islam made each Muslim merchant or traveler an embryonic missionary and the appeal of the religion with its similarities to the African religions was far more powerful than the Christian appeal.
The early Christians of Niger Delta who were against the customs and traditions of the indigenous tribes carried out atrocities such as destroying their shrines and killing the sacred monitor lizards.
The European colonization of Africa is noted to have paved the way of Christian missionaries into Africa. In some cases, the leaders of traditional African religions were persecuted by the missionaries and regarded as the "devil's agents". Ali Mazrui has discussed similar issues in the book The African Condition. A further example of persecution by missionaries is how many of the earliest Christian missionaries to the Shona people, of modern day Zimbabwe, desecrated shrines located in Matonjeni, harassed Shona priests and decried Mwari, the Shona God, as being a fake and inept God. This persecution continued until the Shona were completely prevented from worshipping their God, Mwari, at Matonjeni.
Despite attempts at tolerance and Interreligious Dialogue, in many Christian churches there was a belief that "everything African seems to be pagan", and some argue this view remains today in certain evangelical Pentecostal religious positions. The historical view that Africans had to become "civilized" by slavery, colonialism and Christian missionary activity likely contributed to the intolerance of traditional religions during the colonial period. These views culminated in some colonials rejecting that traditional African faiths were proper religions.
^M. Darrol Bryant, Rita H. Mataragnon, The Many faces of religion and society (1985), Page 100, [books.google.com]:"African traditional religion went through and survived this type of persecution at the hands of Christianity and Islam..."
^Garrick Bailey, Essentials of Cultural Anthropology, 3rd ed. (2013), Page 268, [books.google.com]:"Later, during the nineteenth century, Christian missionaries became active in Africa and Oceania. Attempts by Christian missionaries to convert nonbelievers to Christianity took two main forms: forced conversions and proselytizing."
Festus Ugboaja Ohaegbulam, Towards and Understanding of the African Experience (1990), p. 161, [books.google.com]:"The role of Christian missionaries are a private interest group in European colonial occupation of Africa was a significant one...Collectively their activities promoted division within traditional African societies into rival factions...the picture denigrated African culture and religion..."
^Toyin Falola et al., Hot Spot: Sub-Saharan Africa: Sub-Saharan Africa (2010), p. 7, [books.google.com]:"A religion of Middle Eastern origin, Islam reached Africa via the northern region of the continent by means of conquest. The Islamic wars of conquest that would lead to the Islamization of North Africa occurred first in Egypt, when in about 642 CE the country fell to the invading Muslim forces from Arabia. Over the next centuries, the rest of the Maghreb would succumb to Jihadist armies...The notion of religion conversion, whether by force or peaceful means, is foreign to indigenous African beliefs...Islam, however, did not become a religion of the masses by peaceful means. Forced conversion was an indispensable element of proselytization."
^Black God: The Afroasiatic Roots of the Jewish, Christian, and Muslim Religions, Julian Baldick
^"African traditional religion in the modern world", p. 125, by Douglas E. Thomas
^Molefi Kete Asante, "Encyclopedia of African Religion", Volume 1, 287:
It is this awareness of the limitation of human knowledge of God that explains, in part, the amazingly tolerant nature of African traditional religion and the absence of excommunications and persecution of heretics in the religious history of Africa ..."
^"The Wiley-Blackwell Companion to African Religions", 325, by Elias Kifon Bongmba
^Warfare in African History (New Approaches to African History) Richard J. Reid, Kindle Edition, location 617
^Muslim Societies in African History (New Approaches to African History), David Robinson, Chapter 1.
^"Visions & Revisions: Selected Discourses on Literary Criticism", p. 176, by Emeka Nwabueze
^"Education for Renaissance in Africa- Large Format" by Raphael J.Njoroge, p. 314
^"African Traditional Religion Encounters Christianity: The Resilience of a Demonized Religion" by John Chitakure, p. 77
^"African Religion in the Dialogue Debate: From Intolerance to Coexistence" By Laurenti Magesa, p. 46-47
^"West African Militancy and Violence", by James Gow, Funmi Olonisakin, Ernst Dijxhoorn, p. 31-32, url = 
^"West African Militancy and Violence", by James Gow, Funmi Olonisakin, Ernst Dijxhoorn, p. 32
^Swiderski, Stanislaw. La religion bouiti, Volumes 1 à 2. The persecutions of the Bwiti, organized by the Catholic Church and the colonial government, or even by certain members of the present government, have reinforced the "racial" and religious consciousness of the Bwiti