The couple's daughter, Carol Schuller Milner, said her parents stepped down because they and the board couldn't agree on a deal for housing benefits and fees for using her father's writings and sermons.
"We cannot continue to serve on the Board in what has become an adversarial and negative atmosphere especially since it now seems that it will not be ending anytime soon," Arvella Schuller said in a statement.
Robert Schuller, who is known for the "Hour of Power" broadcast, retired from day-to-day operations in 2006. Last month, the sale of the cathedral to the Roman Catholic Diocese of Orange was finalized in a $57.5 million bankruptcy deal.
Turmoil in the ministry included the firings of Schuller's daughter Gretchen Penner and two sons-in-law in the past week.
The Associated Press contributed to this report.