John Ortberg has resigned from Menlo Church following investigations into his decision to allow his son to work with children despite admitting he was attracted to minors.
He was asked to tender his resignation by the California church's board of elders and agreed to do so last week.
"In recent days and after a process of mutual discernment with John and in consultation with the Presbytery, it is with a heavy heart that the board unanimously concluded that John should resign as Senior Pastor of our church," the board said in a statement.
Ortberg had originally been asked to take a leave of absence from the church last November while an investigation was carried out into his actions.
It was Ortberg's estranged transgender son, Daniel Lavery, who informed the board that Ortberg had allowed a volunteer to work with children despite admitting they were attracted to children.
Lavery then later revealed that the volunteer in question was Ortberg's youngest son.
The first investigation concluded that no child had been harmed by Ortberg's son, and the pastor returned to the pulpit in March.
But after the congregation found out that the volunteer was Ortberg's son, a second investigation was launched earlier this month to supplement the original investigation.
Following this, however, the Menlo Church elders have now asked Ortberg to resign.
Explaining their actions in their statement, the elders said this decision "stems from a collective desire for healing and discernment focused on three primary areas".
"First, John's poor judgement has resulted in pain and broken trust among many parents, youth, volunteers, and staff," they said.
"Second, the extended time period required to complete the new investigation and rebuild trust will significantly delay our ability to pursue Menlo's mission with the unity of spirit and purpose we believe God calls us to.
"Third, in this coming season John needs to focus on healing and reconciliation within his own family."
In his own statement, Ortberg expressed regret over his actions.
"I want to express again my regret for not having served our church with better judgement," he said.
"Extensive conversations I had with my youngest son gave no evidence of risk of harm, and feedback from others about his impact was consistently positive.
"However, for my part, I did not balance my responsibilities as a father with my responsibilities as a leader.
"I am hopeful that my leaving can mark a new beginning in our church's ministry, and will also appreciate your prayers for our family.
"Although I am sad to have my time at Menlo end in this way, you should know that sadness is not the only or even main emotion in my heart. Far more than that, I will carry the memories of seventeen years of ministry and worship and learning and prayer and tears and laughter and spiritual growth that I will cherish as long as I live."