Chief executive Grant Watson has resigned after just under three years with the company, during which it has gone to the brink of collapse and been saved by a rescue package from by its major shareholders.
Synlait chair George Adams said Watson has led the company through a tumultuous time.
"Recent months have seen a long list of urgent challenges for Synlait, and Grant's ably led the team through them. His achievements are extensive and notably include our balance sheet's recent, successful reset."
Watson called Synlait an "amazing and agile company".
"Working with our passionate employees and farmers who care deeply about Synlait's success has been a privilege. Our team's determination and dedication to deliver has also been a real highlight."
Adams said Watson had helped to drive the company's strategy reset to reduce risk, commercialising plant-based production at its Pokeno plant, and looking for new markets in Asia and securing its China market access.
The head of subsidiary Dairyworks, Tim Carter, has been appointed acting chief executive.