After Smith's death, Bernhisel followed Brigham Young and moved west with the majority of the Latter-day Saints.

He settled in Salt Lake City, Utah Territory, in 1848 and continued the practice of medicine.

Bernhisel was selected by Young to represent the interests of the Latter-day Saints before Congress when the Mormon settlers began to consider an application for statehood as the State of Deseret.

Longtime Washington journalist Benjamin Perley Poore described Bernhisel during those years as "a small, dapper gentleman, who in deportment and tone of voice resembled Robert J. Walker": It was very rarely that he participated in debate, and his forte was evidently taciturnity.

Bernhisel was a bachelor until he was 46 years old (March 1845), when he married Julia Ann Haight, the widow of William Van Orden and mother of five children.