In 1944, Baker started working for Ernest Knight, an older white man who had broken his leg. He owned a gristmill and, upon sexually assaulting Lena multiple times, he would keep her there imprisoned for days at a time in “near slavery.” Knight’s son and townspeople disliked their relationship, and tried to end it through threatening Baker. One night an argument between the two ensued, during which Knight threatened Baker with an iron bar. As she tried to escape, they struggled over his pistol and she shot and killed him. She immediately reported the incident and said she had acted in self-defense.

Lena Baker was charged with capital murder and stood trial on August 14, 1944. The trial was presided over by Judge William “Two Gun” Worrill, who kept a pair of pistols in view on his judicial bench. At her trial, Baker testified that Knight forced her to go with him on that Saturday evening of April 29. The town disliked their sexual relationship and the county sheriff had warned her to stay away from Knight, or risk being sent to jail. But she was afraid of Knight’s physical abuse; he had forced relations on her. His son had also beat her on another occasion, warning her to stay away from his father. Baker said she got away from Knight that night and slept in the woods. As she returned to Cuthbert the next morning, Knight cornered her, taking her to the gristmill and locking her in. When Knight returned, Baker told him she was leaving. According to Baker, they “tussled over the pistol,” after he threatened her with an iron bar. She immediately reported it to J.A. Cox, the county coroner who had previously employed her.

Governor Ellis Arnall granted Baker a 60-day reprieve so that the Board of Pardons and Parole could review the case, but in January 1945 it denied Baker clemency. She was transferred to Georgia State Prison at Reidsville on February 23, 1945.

Baker was executed on March 5, 1945. She was buried in an unmarked grave behind Mount Vernon Baptist Church, where she had sung in the choir.

In 1998, members of the congregation arranged for a simple headstone for her grave. That year two articles were published about her case.

In 2001, Lela Bond Phillips, a professor at Andrew College, published a biography titled The Lena Baker Story, which was adapted into a feature film of the same name in 2008. Tichina Arnold played the role of Lena Baker.

In 2003, descendants of Baker’s family began to mark the anniversary of her death and Mother’s Day at her graveside. That year Baker’s grandnephew, Roosevelt Curry, requested an official pardon from the state, aided by the Georgia-based prison advocacy group, Prison and Jail Project.

In 2005, the Parole Board granted Baker a full and unconditional pardon. Commentators have suggested that in 1945, the Board of Pardons and Parole could have lowered her charge to voluntary manslaughter, which would have carried an average 15-year sentence and saved her life.