The Oklahoma City-based charity said Frances Jones, 69, resigned, but her husband Larry said she was fired, The Oklahoman reported Monday.
The charity's board of directors fired Larry Jones about 14 months ago.
"Mrs. Jones has expressed a desire to spend more time on personal matters," the organization said in a statement. "We are grateful for her past service as a co-founder of the organization. We accept her decision to resign and wish her well in all future endeavors."
Larry Jones, 70, who has sued the charity over his dismissal, said his wife's departure was not her idea.
"That's a lie," Jones said. "They asked her to leave. I'm going to clean up the lie. They asked her to leave last September. That's all I want to say. I'm tired of their lying. I'm just downright tired of all the lies that they've told."
Sources told the newspaper the charity "bought out" Frances Jones's two-year contract. Her salary was $200,000 annually.
The couple built the Christian relief organization into one of the most recognized charities in the nation, with donations reaching $1.9 billion a year.
Jones said her last day was Dec. 31 and refused to comment on the matter.
"It really doesn't matter now," she said.
Her attorney, Gary Richardson of Tulsa, said his client's departure was based on timing.
"She was ready to leave," Richardson said. "I think they were ready for her to leave. We were able to work out a mutual agreeable condition."