The Rev. Wes Feltner has resigned his position at a Burnsville megachurch, following allegations that he had inappropriate sexual relationships with two 18-year-olds when he was in his 20s and serving as youth pastor at the Indiana church they attended.

Feltner, 41, was a popular pastor at Berean Baptist Church in Burnsville, which has experienced tremendous growth in the six years since he started there and had recently opened a second location in Lakeville.

Members of the congregation learned of Feltner’s resignation this weekend when a statement from church elders was read at services.

“After much prayer and deep consideration for his family and the mission of Berean Baptist Church, Pastor Wes Feltner has submitted his resignation,” the statement said. “Pastor Wes and his family are entering a period to seek healing and we will walk with them during this process.”

Earlier this month, Berean Church officials said they had hired an outside firm to investigate the women’s claims while Feltner took a leave of absence. That investigation continues and Feltner is cooperating, according to the Berean elders’ letter.

JoAnna Hendrickson and Megan Frey, both now 35, say Feltner used his position of authority inappropriately and manipulatively 17 years ago, when the women were in their high school and college years.

They detailed their allegations on a website they created, where they discussed their relationships with Feltner and the emotional struggles they’ve had as a result.

Hendrickson and Frey said Friday they couldn’t comment on Feltner’s resignation because he is still under investigation by the church.

In an e-mail this month to the Star Tribune, Feltner said that while some parts of the women’s statements were true, others were not. He said he had offered to speak with them about the matter, including with a mediator, but they declined. He said he would address the allegations in more detail after the investigation was finished.

In their statement, church elders said it was “necessary to complete this investigation to be able to speak into the healing process for Wes and for all involved. We also know that this season has opened wounds in our faith family and we are developing a plan to make resources available to help heal our faith family.”

Feltner was in the running for a pastor position at a church in Clarksville, Tenn., in October when an acquaintance of the women and Feltner told the church about the women’s stories. That church is no longer considering Feltner for the position.

He also has been suspended from teaching at Southern Baptist Theological Seminary in Louisville, Ky., which he had attended as a student.

Some evangelical churches, including a number that belong to the Southern Baptist Convention, have become embroiled in controversy after women have come forward with stories of sexual abuse and misconduct at the hands of church leaders. Survivors of the abuse coined the hashtag #churchtoo, a takeoff on the #metoo movement.

Berean is not part of the Southern Baptist Convention, though the church where Feltner was youth pastor when the alleged relationships occurred belongs to the denomination.

Ashley Easter, a North Carolina-based advocate for survivors of church abuse, said that though the women weren’t minors at the time of the alleged relationships, “there’s still a distinct power differentiation between clergy and lay people. In many denominations, they’re looked at as being the man or woman who speaks for God.”