"[12][13] Despite being plagued by incidents such as the 1953 Short Creek raid, Johnson's thirty-two-year tenure as senior member of the Priesthood Council has been characterized as "a time of stability, growth, financial success, and greater public acceptance.

While acting as Prophet, Johnson dismissed J. Marion Hammon and Alma A. Timpson from the Council of Friends for their opposition to the "One Man Doctrine".

Following Johnson's death in Hildale, Utah, and burial at the Isaac W. Carling Memorial Park on November 25, 1986, Rulon Jeffs succeeded him as leader of the FLDS Church.

Although Johnson had been very ill and unable to mingle among the people for several years, his passing created a "climate of upheaval" within the community, during which the church became increasingly authoritarian.

In recent years, Johnson's tenure as Prophet has become a focal point for Mormon fundamentalists disaffected with the modern FLDS Church.