In September 1858 Cannon was called to preside over the Eastern States Mission; his duties included directing westward immigration and quelling falsehoods concerning Utah and the Mormons. The following year, he was sustained an apostle to fill the vacancy created by the murder of Parley P. Pratt.

Greater responsibilities followed when Cannon was sent to preside over the European Mission. His specific duties were to direct emigration and supervise the printing of the Millennial Star. However, within a few months he was notified that he had been elected as one of Utah Territory's two congressional representatives and was immediately needed in Washington, D.C., to assist in Utah's 1862 bid for statehood. At the adjournment of the 1862 congressional session, he returned to Europe for two years to continue his assignment as presiding authority.