He resigned from the Quorum of the Twelve due to his unwillingness to support the church's abolition of plural marriage.

With the death of apostle Marriner W. Merrill in early February of the next year, there were three vacancies in the Quorum of the Twelve.

[5] As a result, three new apostles were called to replace them and Merrill: George F. Richards, Orson F. Whitney, and David O. McKay.

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.

His son, Samuel P. Cowley, by his wife, Luella Parkinson, was an FBI agent best known for his death at the hands of Lester "Baby Face Nelson" Gillis in 1934.