Schappert's resignation did not arise from "any disagreement with the Company on any matter relating to the company's operations, policies or practices," the filing said.
The social gaming company behind "Farmville" confirmed earlier this month that Schappert had already ceded many of his responsibilities while the company shuffled its top management ranks in the wake of a disastrous second quarter.
Zynga's COO quits as stock continues slide
Zynga elevated David Ko, its chief mobile officer, and Executive Vice President of Games Steve Chiang, to top positions overseeing game development alongside Chief Executive Officer Mark Pincus. But the company did not immediately name a replacement for Schappert on Wednesday.
"John has made significant contributions to the games industry throughout his career and we appreciate all that he has done for Zynga," Pincus said on Wednesday in a statement. "John leaves as a friend of the company and we wish him all the best."
Zynga reported a net loss for its second quarter in late July and cut its full-year earnings per share forecast, news that sent shares down roughly 40 percent and attracted a wave of shareholder lawsuits accusing the company of misguiding investors.
The company blamed changes to Facebook's algorithm, which helps boost the popularity of Zynga's social games, and delays in its pipeline of games.
The hiring of Schappert in May 2011 was viewed as a coup for Zynga. He received a base salary of $300,000 last year, as well as cash and stock bonuses.
With Ko's ascension, Zynga has hoped to prioritize the development of games on smartphones, a format that is viewed as critical to the company's future.
Zynga, one of several Internet startups that debuted with fanfare in late 2011, closed on Wednesday at $2.95 and slipped further in after-hours trade. Its stock debuted in December at $10.