After concerns were raised about his behaviour by a group of pastors, including author John Ortberg, the Chicago Tribune put together an investigation which looked at various allegations made over a number of years including suggestive comments, extended hugs, an unwanted kiss and invitations to hotel rooms.
Hybels continues to deny the accusations but has apologised for reacting with anger.
Announcing his immediate resignation, he said: "My first response to some of these recent accusations was anger. I confess to feeling very angry these last few weeks as I watched harmful accusations fly around without accountability. I felt attacked and knew that my loved ones and this church family would be affected.
"I sincerely wish my initial response had been one of listening and humble reflection. If I could go back, I would have chosen to listen first, and then to seek to learn and understand. I apologise for a response that was defensive, instead of one that invited conversation and learning."
He also apologised for being "unwise" and potentially misleading people.
He said: "I realise now that in certain settings and circumstances in the past I communicated things that were perceived in ways I did not intend, at times making people feel uncomfortable. I was blind to this dynamic for far too long. For that I'm very sorry."
Hybels had planned to pass on the leadership of the church in October.
In his resignation statement he says he'll continue to worship at Willow Creek.
"If you are wondering if I am going anywhere, after a season of reflection, I intend to rejoin all of you here in the Willow congregation," he said. "Willow will always be my home church."
In 2014, elders at the church found him to have done nothing wrong after a woman who made the claim of an affair admitted she had lied.
Since then, according to the Chicago Tribune, other women have made serious claims. In one case a woman suggested Hybels summoned her to his hotel room and kissed her while on a trip to Sweden in 1998.
Another accused him of "a lingering hug" which made her feel uncomfortable while another claim suggested he'd invited a woman to his house, but only while his wife was away.
Hybels has also resigned from the board of the Willow Creek Association, which supports a network of thousands of churches globally, and will not host the Willow Creek Leadership Summit in August.
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