Alliance Trust Savings chief executive Patrick Mill is leaving the platform as advisers continue to report service issues during replatforming.
Mill has run ATS, which has set a precedent in the platform market for charging fixed fees, since June 2012.
However, the platform has recently come under criticism from advisers as issues with replatforming have led to service issues.
ATS was planning to launch a new platform to advisers in the third quarter of 2016.
The firm had apologised to advisers over “frustrations” they were having with the delays.
Issues advisers have reported to Money Marketing include missed income payments, delays opening new accounts, valuations being shown in dollars, and application forms going missing.
In August, the platform lost chief operating officer Allison Fower after just eight months with the firm.
The platform was one of few to make a profit in 2016, turning a £1.2m gain after a £5.2m loss for 2015.
Assets under administration jumped 60 per cent to £13.6bn by the end of 2016.
Mill was previously a sales director at Prudential.
Former FCA senior adviser Ron Baxter will be taking over ATS on an interim basis.
Baxter says: “On behalf of the board, I would like to extend our thanks to Patrick for his contribution over the last 7 years, during which time assets under administration have increased to over £15bn. We wish him well in his future endeavours. We have a strong management team and excellent staff to take the business forward”