COBA will immediately commence a national search for a new CEO, which will be overseen by the board.
COBA chair Wendy Machin said that Mr Degotardi had made a significant contribution to COBA and the sector and would be missed.
“The board acknowledges the outstanding contribution that Mark has made to COBA and the sector over more than 14 years with the organisation,” Ms Machin said.
“COBA has a stronger strategic focus and has achieved significant wins on behalf of the sector under Mark’s leadership,” she said.
“COBA is recognised as a strong and professional voice on behalf of its members, and Mark leaves the organisation stronger than when he took on the role of CEO.
“Mark’s skills, experience, knowledge and professionalism have been key drivers of COBA’s success.”
Mr Degotardi acknowledged the support of the board and members during his time as CEO and paid tribute to the professional COBA team.
“It has been my privilege to serve as COBA’s CEO,” said Mr Degotardi. "Customer-owned banking stands out as the strong, ethical, consumer-focused alternative in retail banking, and it has been an absolute pleasure to advocate on behalf of the sector.
"Customer-owned banking changes peoples’ lives for the better every day. This wasn’t the reason I first came to COBA, but it is the reason I have stayed for over 14 years.
“It is, however, the right time for me to seek a new challenge, and for COBA to look for fresh perspectives to help the industry to continue to grow.”
Mr Degotardi will finish at COBA on 31 August 2017.
Dominic Dunn, COBA’s head of corporate and business services, will be acting CEO from 1 September.