Although Roman Catholic influence had been present in the area sometime before their arrival, in fact a sizable Nimíipuu Catholic community was to develop later, the first permanent missionaries to the Nimíipuu were Presbyterian. Rev. Samuel Parker passed through their territory in 1832. He was well received, but was more interested in further exploring the Snake and Columbia rivers than remaining with the Nimíipuu.

The year of 1831 was momentous for the Nimíipuu. An Indian delegation consisting of four Nimíipuu journeyed to St. Louis seeking the superintendent of Indian affairs, who happened to be William Clark. The delegation was made up of Wep-tes-tse-mookh Tse-mookh (Black Eagle), Ka-ow-poo (Man of the Dawn), Ta-weis-se-sim-nihn (No Horns) and Heh-yookts Toe-nihn (Rabbit Skin Leggings). Being only able to converse in signs, they requested the "black book" and the "black robes" for their people. Many believe they were, in fact, seeking the bible and the Jesuit missionaries. Others feel they desired a portion of the white man's power that resided in their writing and "religion." And it may simply have been that the missionaries were sought out for the material possessions they could provide. Whatever the motivation, only Rabbit Skin Leggings was able to rejoin his family, who were hunting in western Montana, where they were told of the success of the journey. The other members of the journey died of illness, in St. Louis or upon returning. Rabbit Skin Leggings himself never did reach his homeland, as he too died, killed at the hands of the Blackfeet in Montana.

In the soyaapo world, news spread quickly about the Nimíipuu "request for religion." Protestant missionaries responded and journeyed west in 1836. Soon after, Henry and Eliza Spalding, who mistakenly believed the Nimíipuu lacked a "religion" all together, settled not far from the mouth of Lapwai Creek. They held lofty goals of Christianizing, "educating," and converting the Nimíipuu to the white man's ways. Asa Smith, another missionary, settled along the Clearwater River at Kamiah from 1839 to 1841. As a linguist and a missionary, he sought to learn the Nimíipuu language and compile a dictionary. Marcus and Narcissa Whitman went on to Fort Walla Walla and Cayuse country, and established a separate mission at Waiilatpu, "place of the rye grass" along the Walla Walla River.

The missionaries engaged in several important cultural innovations including the introduction of non-Indian medical practices, establishment of farming, and the construction of mills in hopes of settling the Nimíipuu around the mission settlements. A printing press and instruction in reading and writing were also introduced in accordance with the Protestant tradition of ensuring all people have access to a bible.

Initially, there were good relations between the missionaries and the Nimíipuu. The missionaries were fed and labor was provided to help them build their log homes, schools and churches. People attended services, hymns were sung and, in the day school, reading and writing were taught. Crop seeds and farm equipment was distributed. Though Spalding was unskilled as a physician, medicines were dispensed and blood-letting skills taught to the Nimíipuu. Among the first new converts to be baptized were Tamoostsin, whom Spalding called Timothy, and Tuekakas, a leader of the Wallowa band, who was named by the missionaries, Joseph (whose son would carry his father's name in years to come). Along with Lawyer, Timothy was of particular assistance and a strong supporter of the missionaries.

But soon relations began to sour. Spalding was a very stern and bitter man, whose temper easily ran short. Some years before, he had even proposed marriage to, but had been rejected by Narcissa. Though helping develop the first book written in the Nez Perce language (an instructional primer on religious teachings for children), on Idaho's first printing press, Spalding himself never successfully learned the language of the people he sought to convert. Misunderstandings frequently followed. Spalding saw all traditional spiritual beliefs as sorcery and evil, along with horse racing, gambling, dancing, singing and drumming, and made every effort to stamp out these practices. Not to follow the new teachings meant damnation to "hell," a new and disturbing concept for the Indian.

In one example of his attempts to win converts, before Spalding would distribute potato seed to the Nimíipuu he would cut the eyes out of those potatoes he intended to give "heathens." Proclaiming the favor looked upon them by God, Spalding would point to the successful potato harvest Christianized Nimíipuu had obtained, while "heathens" produced nothing. Many Nimíipuu were either confused by Spalding's behavior or outright offended by the zeal and fervor of the attack on their most cherished traditions.

In addition, tensions between the Whitmans and the Cayuse steadily grew, as Marcus seemed more interested in bringing settlers into his country than assisting the Indian. Large numbers of emigrants were crossing through Indian lands on their way west, some settling on the land and few of them were aware of Indian rights to the land.

In an attempt to better control the Nimíipuu, Spalding sought to centralize authority with the tribe by having the tribe select a single chief. Spalding found it very difficult to work with the headmen of each band, each virtually independent of the other. Under great pressure, Ellis, who had been taught at the Red River School and the grandson of Red Grizzly Bear, was selected. Ellis spoke English and was a strong supporter of the missionaries. But among many of Nimíipuu Ellis was too young to be a headman, only 32 years old, and many non-Christians refused to recognize him as the head chief. This imposition of an alien political structure onto the Nimíipuu only served to further the growing tension and rift between the "Christian Nez Perce" and whose called by the missionaries, the "heathens." This schism among the Nimíipuu would characterize relations into the twentieth century, causing intense rivalries between family members and contribute to the erosion of traditional Nimíipuu traditions and practices.

During the fall of 1847, a measles epidemic spread among the Cayuse, introduced by emigrants passing through the area. Nearly half the Cayuse died. While both Whitman and Spalding dispensed medicines to the people, some interpreted their actions as actually helping spread the "death." On November 28, 1847 the Whitmans and 11 other whites at their mission were killed by the Cayuse. News of the massacre spread, and soon after the Spaldings left Nimíipuu.

This would not end missionary influences among the Nimíipuu, as Spalding would return in the 1870s and the two Presbyterians missionary sisters, Kate and Sue McBeth, would begin their efforts at the same time. The McBeth sisters continued the crusade of eliminating all aspects of the "heathenish" behavior among the Nez Perce. Only with the their passing, Sue dying in 1893 and her sister Kate in 1915, did the zeal and fervor toward extinguishing traditional Indian culture in favor of "civilization" begin to subside.

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