Merrill joined the LDS Church in 1852 and moved to Salt Lake City, Utah Territory the following year. In 1860, he was among the first to move to Richmond, Utah where he would eventually operate a large farm and start a grist mill. He also worked as a contractor in the construction of the Utah and Northern Railway. He was a member of the territorial legislature for two terms.
Merrill became the first president of the Logan Utah Temple in 1884 and a member of the Quorum of the Twelve Apostles on October 7, 1889. He served in both offices in the church for the rest of his life.
At a family reunion in 1935 his family numbered 797 descendants, of which 291 were grandchildren, 429 great grandchildren and 31 great grandchildren. During the time of the polygamy raids, he lived in his bedroom on the second floor, in the west tower, and never left the Logan Temple for weeks at a time.