Reports of Cowley's continuing involvement in new plural marriages led to his
priesthood being suspended by the church on May 11, 1911. This rare and virtually unique disciplinary procedure was used for Cowley because the members of the Quorum of the Twelve disagreed about whether to leave him undisciplined, to disfellowship him, or to excommunicate him. After his priesthood was suspended, Cowley's name continued to be linked with plural marriage over the next several years. As late as the early 1920s, Cowley was meeting with excommunicated polygamists as the early
Mormon fundamentalists began to coalesce at the Baldwin Radio Plant in Salt Lake City. In the mid-1920s, Cowley broke all ties with the polygamous dissenters. His priesthood standing in the LDS Church was restored on April 3, 1936, which was nearly 25 years after it had been suspended. Cowley was never restored to his position in the Quorum of the Twelve. He died in his home in
Salt Lake City, Utah, from
uremia resulting from kidney failure. He was buried at
Salt Lake City Cemetery. ==Honors and children==