Morgan was born in Greensburg, Decatur County, Indiana, and served as a sergeant in the Union Army in the 123rd Illinois Volunteer Infantry Regiment during the American Civil War.

After graduation, he traveled to Salt Lake City on business, and decided to permanently relocate there.

The college provided a number of innovations, including Utah's first free public library, and the first school run by a non-Mormon.

[1] On November 26, 1867, Morgan joined the LDS Church and on October 24, 1868 he married one of his former students, Helen Melvina Groesbeck.

During his term as mission president he was involved with attempts to help the Catawba tribe move to the west to be with the rest of the Saints.