Cumming's assumption of office began with the controversy and difficulties known later as the Utah War. Forced to winter near Fort Bridger, Cumming had begun to take a somewhat moderate position on the Mormon question by the time he actually arrived in Utah in the spring of 1858. This placed him in opposition to the three hardline judges and Johnston, who as army commander had been badly embarrassed by Mormon resistance. Despite initial Mormon jeers, Cumming's essential moderation was quickly recognized by Mormons with whose efforts to maintain a degree of self-determination he often sided in the give-and-take that characterized territorial politics in the wake of the Utah War and the Mountain Meadows Massacre. Given the oncoming Civil War, this was a particularly difficult time for Cumming, a Southerner. Nevertheless, he occupied the gubernatorial chair with dignity and fairness, and even achieved a degree of success in helping to define the nature of political authority in the federal territorial system that was emerging in the area that had been taken from Mexico.
With Governor Cumming was his wife Elizabeth, a sensitive and observant lady. She shared the difficult winter near Fort Bridger and with her husband occupied the William Staines home (or Devereaux House as it was later known) during the three years of their stay in Utah. Her letters provide a rare insight into events of that time, and record her impressions of the Utah landscape and social life as well as politics among the federal appointees, especially during 1857 and 1858.
At the end of his four-year term Cumming returned to Washington, D.C. He settled the details of his administration and prepared to return to Augusta. However, his return was postponed by the Civil War until the summer of 1864. His wife passed away in 1867, and Cumming himself died in 1873 at the age of seventy-one. His term as governor of Utah Territory had been one in which the issues of self-determination, shared sovereignty, and territorial/federal relationships were tested as in few other times in the long American effort to create a democratic substitute for centralized colonial rule. Although many other distinguished individuals occupied the Utah's gubernatorial chair during territorial times, few of them served Utah better.