In 1869 and 1870, Cannon served a second mission in the Eastern United States. In April 1876, Cannon became president of the Salt Lake Stake of the LDS Church. He served in this position until April 1, 1904. After his time as stake president, Cannon served as a patriarch in the church.
Like many early members of the LDS Church, Cannon practiced plural marriage. Cannon was the appellant in the case of Cannon v. United States, which was decided by the United States Supreme Court in 1885. Cannon had been convicted under the Edmunds Act of unlawful cohabitation with more than one wife and sentenced to six months' imprisonment and a $900 fine. Cannon appealed his conviction on the grounds that he had immediately ceased having sexual relations with the two wives he was accused of cohabiting with after polygamy was criminalized. The Court rejected Cannon's argument, holding that "[c]ompacts for sexual non-intercourse, easily made and easily broken, when the prior marriage relations continue to exist, with the occupation of the same house and table and the keeping up of the same family unity, is not a lawful substitute for the monogamous family which alone the statute tolerates."