Cooley suspected his second wife, Ella Mae Cooley (née Evans), 38, who had been a singer in his band before they married 15 years earlier, of repeatedly being unfaithful. In March 1961, she told a friend she had had an affair with Roy Rogers in 1952 or 1953. She soon asked Cooley, who had had many of his own affairs, for a divorce. On March 23, Spade Cooley filed for divorce, citing "incompatibility" and seeking custody of their three children, Melody, Donnell Jr. and John.
On April 26, 1961, Cooley was indicted by a Kern County grand jury for the murder of his wife on April 3 at the couple's Willow Springs ranch home. Cooley's then 14-year-old daughter, Melody, recounted to the jury how she was forced by her father to watch in terror as her father beat her mother's head against the floor, stomped on her stomach, then crushed a lit cigarette against her skin to see whether she was dead. Cooley claimed his wife had been injured by falling in the shower.
He was defended by attorney P. Basil Lambros in what was the longest case in county history at the time, and was convicted of first-degree murder by a Kern County jury on August 21, 1961 after unexpectedly withdrawing an insanity plea. He was spared death in the gas chamber and sentenced to life in prison.