The move is part of a board succession planning process being undertaken by Brains’ chairman, John Rhys.
Waddington will stay in his current role for the next six months to allow for the recruitment of his successor.
The company said he would continue to work with the teams at Brains to deliver the ongoing business plan and oversee the company’s move to its new brewery and head office facility.
The existing Brains site is being developed in partnership with Rightacres Property as a 2.5m sq ft office, leisure and residential development.
Waddington was responsible during his 17 years in making “significant investment” in the quality of its pub estate, growing its food business “exponentially”, acquiring and subsequently rolling out Coffee#1 and sponsoring the Welsh Rugby Union and Football Association of Wales.
Rhys said: “Scott has been a distinguished leader of the company over the past 17 years. I have enjoyed working with him during that time and look forward to doing so over the coming months while we search for the right person to lead the business into the next stage of our development”.
Waddington added: “It has been a privilege to lead such an iconic Welsh company and I would like to thank all my colleagues over the years for making my time here so rewarding and enjoyable.
"With a number of our strategic priorities now reaching their conclusion, this felt like the natural time for me to move on to new challenges and to hand over to a new leader to take this great business on to its next stage of development. I look forward to working with John to ensure a smooth handover to my successor later this year.”