The three Prairie provinces adopted a system based on Ontario's with a dominant Protestant system, and smaller Catholic ones.

Manitoba Schools Question
In 1891, Manitoba moved to eliminate the Catholic board, sparking the Manitoba Schools Question. It demonstrated the deep divergence of cultural, religious and language values and became an issue of national importance. The Catholic Franco-Manitobains had been guaranteed a state-supported separate school system in the original constitution of Manitoba, such that their children would be taught in French. However a grassroots political movement among English Protestants from 1888 to 1890 demanded the end of French schools. In 1890, the Manitoba legislature passed a law removing funding for French Catholic schools. The French Catholic minority asked the federal government for support; however, the Orange Order and other anti-Catholic forces mobilized nationwide to oppose them. The federal Conservatives proposed remedial legislation to override Manitoba, but they were blocked by the Liberals, led by Wilfrid Laurier, who opposed the remedial legislation because of his belief in provincial rights. The Manitoba Schools issue became an issue in the Canadian federal election of 1896, where it worked against the Conservatives and helped elect the Liberals. As Prime Minister, Laurier implemented a compromise stating that Catholics in Manitoba could have their own religious instruction for 30 minutes at the end of the day if there were enough students to warrant it, implemented on a school-by-school basis.

The Catholic archbishop of Edmonton, Henry Joseph O'Leary had a considerable impact on the city's Catholic sectors, and his efforts reflect many of the challenges facing the Catholic Church at that time. During the 1920s, O'Leary favored his fellow Irish and drastically reduced the influence of French Catholic clergy in his archdiocese and replaced them with Anglophone priests. He helped to assimilate Ukrainian Catholic immigrants into the stricter Roman Catholic traditions, extended the viability of Edmonton's separate Catholic school system, and established both a Catholic college at the University of Alberta and a seminary in Edmonton.

In 1892 Alberta adopted the Ontario schools model, emphasizing state-run institutions that stressed the English language, English history and English customs. The Catholic community, under the control of Irish, joined the British Protestant community in these new policies, despite the complaints of the French-Canadian minority. Predominantly francophone communities in Alberta maintained some control of local schools by electing trustees sympathetic to French language and culture. Such groups as the Association Canadienne-Française de l'Alberta expected trustees to implement their own cultural agenda. An additional problem francophone communities faced was the constant shortage of qualified francophone teachers during 1908-35; the majority of those hired left their positions after only a few years of service. After 1940 school consolidation largely ignored the language and culture issues of francophones.

Canadianization of immigrants
After 1870 numerous non-Anglophone immigrants arrived from Europe, including Germans, Ukrainians, Scandinavians and many others. Large numbers headed to the attractive free farms in the Prairie Provinces. Education was a central factor in their assimilation into Canadian culture and society. An important indicator of assimilation was the use of English; the children of all immigrant groups showed a strong preference in favour of speaking English, regardless of their parents' language. From 1900 to 1930, the governments of the Prairie Provinces faced the formidable task of transforming the ethnically and linguistically diverse immigrant population into loyal and true Canadians. Many officials believed language assimilation by children would be the key to Canadianization. However, there was opposition to the direct method of English teaching from some immigrant spokesmen. English-language usage in playground games often proved an effective device, and was systematically used. The elementary schools especially in rural Alberta played a central role in the acculturation of the immigrants and their children, providing, according to Prokop, a community character that created a distinctive feature of Canadian schools glaringly missing in the European school tradition.