Longbottom is planning to leave the business and pursue interests abroad however, he will remain a shareholder and will work alongside founder and chairman Ian Payne to ensure a smooth succession.
Current president and chief operating officer of BrewDog, David McDowall will succeed Longbottom at Stonegate.
McDowall has been at the craft beer bar operator and brewing business since 2015 when he was then appointed managing director of its bars.
He is expected to join Stonegate, which has 4,500 pubs, early next year when he will work alongside Longbottom until spring to aid facilitating an orderly handover.
Longbottom said: “It has been an honour to lead the team which has taken Stonegate from a challenger brand to industry leader in just eight years.
“From our pubs and bars to our people, the talent, passion and pride within the business is second to none and I have every confidence there are even more exciting times to come.
“It’s been an amazing journey but the time is now right for me to pursue other interests abroad. As a shareholder and a fan, I will be supporting the business from afar and wish Ian, David and the wider team continued success.”
Stonegate Group chairman Ian Payne said the board thanked Longbottom for his “significant contribution” to the company’s success over the past eight years.
He added: “During this time, he has been a much-valued member of the senior team in building Stonegate Group into the leading pub and bar business it is today.
“Looking to the future, he leaves Stonegate in excellent health and trading extremely well. The board is confident McDowall will continue to drive Stonegate forward and take advantage of the many opportunities ahead.
Incoming CEO McDowall outlined his thoughts on his new appointment and what the future holds for the business.
He said: “Stonegate is an outstanding business with a clear strategy, highly capable management team and hugely exciting future.
“I am passionate about pubs and the wider brewing sector and am looking forward to joining the team and further unlocking the clear potential of this great business.”