[citation needed] Johnson was then ordained an elder on October 25, 1831 and a high priest of the church on November of that same year.

In response to a revelation given on January 25, 1832, Johnson joined Orson Pratt on an evangelizing mission which took them through the eastern United States.

In the summer of 1834, Johnson marched with the Zion's Camp expedition which hoped to restore Latter Day Saints in Missouri to their lands in Jackson County.

The church held a high council trial on September 3, 1837, which ejected Johnson, his brother Luke, and John F. Boynton from the Quorum of the Twelve.

Boynton explained that his difficulties with the church resulted from "the failure of the bank" which he had understood "was instituted by the will and revelations of God, and he had been told that it would never fail".

Johnson replied on April 12 that "I should not condescend to put my constitutional rights at issue upon so disrespectful a point, as to answer any of those other charges until that is withdrawn & until then shall withdraw myself from your society and fellowship.

"[7] Brigham Young reported that Lyman later lamented leaving the church, though he never rejoined: I would suffer my right hand to be cut off, if I could believe it again.

In Iowa, Johnson became one of the founding figures of Keokuk, along with his brother Luke, contributing to the town's early development.