The reasons for the massacre are complex, but center around a wartime hysteria that had built up in Utah with the announcement in July 1857 that a federal army was en route to Utah to put down an alleged Mormon rebellion. Rumors also circulated that members of the Fancher party had stolen from the Mormons, poisoned their reservoirs, and boasted of their role in the assassination of Joseph Smith.

After the massacre, John D. Lee remained an active leader in Mormon affairs in southern Utah. However, by the late 1860s, questions about the massacre became more and more difficult to avoid, and in October 1870 Brigham Young excommunicated Lee from the Mormon Church for his role in the affair. Lee was the only one so punished and would later maintain that he became a scapegoat to take the public pressure off the more responsible Mormon leaders.