In 1849 he rejoined his family in Farmington, Utah. At Farmington, he served one term as county sheriff, emerged as an officer in the Nauvoo Legion, and acquired a considerable reputation as a livestock man. In 1857 he outshone more famous figures Orrin Porter Rockwell and Robert Taylor Burton in leading a militia force against the supply trains and livestock of the approaching Utah Expedition under Albert Sidney Johnston. Burning several wagon trains and seizing 1,400 animals, he was instrumental in forcing the army to winter near Fort Bridger. Later, under an appointment from President Abraham Lincoln, he commanded a volunteer unit guarding the telegraph line in northern Utah and Wyoming during the early part of the Civil War.
Like many Mormons of his era, Smith was a polygamist, taking in all eight wives. Although he was reputed to be have an explosive temper and to be harsh with his wives and children, his was a close family characterized by loyalty and intrafamilial business associations as his sons and daughters matured.
In 1876 he led a colonizing mission to the Little Colorado River in northern Arizona. For this pioneering venture his decisive and hardbitten character proved to be both a boon and a cause of friction. He quickly confronted jurisdictional problems related to Brigham Young's sometimes ambiguous assignments. At Sunset, near present Winslow, Arizona, he became president of the Little Colorado Stake as well as president of the Sunset United Order, in which he was the dominant figure. He built large herds and bred excellent strains of horses but also quarreled with his fellows over the distribution of property, contributing to much discord and a disputed settlement of the order's affairs in 1886. Enmity lingered for generations among the families of the participants.
After 1886 Smith's associations with the Mormon community cooled as he increasingly devoted his energy to ranching at Tuba City and elsewhere in northern Arizona. Yet, by inclination and the fact that polygamists had little other recourse, he remained a committed Mormon. During his last years, relations with his Indian neighbors became increasingly tense as the rangeland around Tuba City was overgrazed. In 1892 Smith shot several Navajo sheep that had been turned into a meadow he had fenced. A Navajo herder in turn shot several of Smith's cattle. Finally the two exchanged shots with result that the old Mormon was mortally wounded. He was buried near the contested pasture. A decade later, his remains were returned to Farmington, where his grave became something of a symbol of the Mormon pioneer as frontiersman, soldier, and Indian fighter.