The mission was started in 1843 by Presbyterian minister Robert Loughridge at Coweta, then the capital of the Creek Nation, Indian Territory.

For a time the Creek people had resisted Protestant religious missions and their related schools, outlawing Christianity and preaching because it disrupted their traditional culture.

Loughridge later wrote to the US Indian agent for the Creek, Colonel James Logan, describing the beginning of his work with the Creek people: "Although the old chief at first had a manifested some fears of our religious influence interfering with their old customs, yet he gave us a cordial welcome, and requested me to locate the mission in his town.

As soon therefore as it was ready for use, my wife commenced teaching a school of fifteen or twenty children, and the neighbors were invited to attendance at the Mission, while the most of them were devotedly attached to their old customs and superstitions.

"The school operated for about 3 months until sickness and a lack of adequate accommodations resulted in Loughridge temporarily closing it.

[2] After the American Civil War broke out, the Presbyterians abandoned the Koweta Mission and left the Territory, as did other missionaries.

During the war years, most missionaries abandoned the schools and churches they had started among the tribes, but many children had received some education.

The Creek developed a tribal school system funded from federal annuities paid following their removal to Indian Territory.