Willard, Jennetta, and their son left England in April 1841 and settled in Nauvoo, Illinois, where Willard served as a land agent, a member of the city council, and editor of the Times and Seasons. He also was appointed the general clerk and recorder of various community organizations, including the city council and the Nauvoo Temple. In December 1842 he was called to be the LDS Church Historian and Recorder, a position he held until his death.

In 1841 Joseph Smith asked Willard to be his private secretary. In this capacity, he recorded much of the Mormon prophet's activities. He was with Joseph Smith, Hyrum Smith, and John Taylor in Carthage jail when Hyrum and Joseph were murdered. He supervised the removal of their bodies and gave counsel to the church during that troubled time.

As LDS Church historian, he was responsible for keeping the diary of Joseph Smith and was greatly involved in the writing of the history of Joseph Smith. He wrote a total of 1,884 pages of that history, which later was edited by B.H. Roberts and published as the History of The Church of Jesus Christ of Latter-day Saints.