Driscoll, whose church grew to attract more than 12,000 at branches across five states, submitted his resignation Tuesday as elder and lead pastor, concluding "it would be best for the health of our family, and for the Mars Hill family, that we step aside from further ministry at the church," according to the Mars Hill website.
The church currently has multiple branches in Washington, and one location each in Oregon, California and New Mexico. Last month it closed its Phoenix location as a Mars Hill church.
His resignation came after a group of church elders recently ended an investigation into a series of formal charges brought against him.
The church's board said on its website Wednesday that Driscoll was not asked to resign, and that they were surprised to receive his resignation letter.
Driscoll took a leave of absence in August so church leaders could investigate whether he was fit to lead, following accusations that he bullied members, threatened opponents, lied and oversaw mismanagement of church funds, the Seattle Times has reported.
The church said Wednesday that its lengthy investigation found Driscoll has been "guilty of arrogance, responding to conflict with a quick temper and harsh speech, and leading the staff and elders in a domineering manner."
The board said that while it believes Driscoll needs to address those areas in his life, "we do not believe him to be disqualified from pastoral ministry."
The church noted that Driscoll, the only pastor it has known since it was founded 18 years ago, was never charged with immorality, illegality or heresy. It said most of the charges involved the domineering style of leadership, and that they found some accusations "unfair or untrue."
In response to an interview request, church spokesman Justin Dean wrote in an email: "At this time we don't have any additional details." He referred back to the church's statement posted on its website.
Other charges had previously been addressed by Driscoll, the church noted.
The bestselling author has been accused of plagiarism and criticized for his stance against homosexuality and female preachers.
In July, Driscoll apologized for crude comments he made posting under an alias in an online discussion forum 14 years earlier, in 2000, the Seattle Times reported.
Since 1996, the church has attracted thousands of followers in 15 branches in five states. Last month, the church announced it was closing some of its branches and making plans to lay off dozens of employees. The Seattle Times reported that financial problems in the wake of falling attendance forced the cutbacks.
Combined attendance at all Mars Hill branches had dropped from more than 12,000 a week at the start of the year to less than 9,000, a church spokesman said last month.
The board now is planning for the future.
"We would ask for patience as we now make plans for the first transition of pastoral leadership in the history of Mars Hill Church," the church's board said on its website.