In a statement on Friday, the soft-drink producer and long time World Cup sponsor said FIFA President Joseph Blatter should "step down immediately so that a credible and sustainable reform process can begin in earnest."
Coca-Cola said the world soccer body "needs comprehensive and urgent reform" that can only be achieved through an independent approach.
For its part, McDonald's said, "We believe it would be in the best interest of the game for FIFA President Sepp Blatter to step down immediately so that the reform process can proceed with the credibility that is needed."
Fellow sponsor AB InBev agreed, calling Blatter's presence "an obstacle in the reform process."
The beer maker has been actively engaged in the FIFA reform process as part of a sponsor group that includes Adidas, Coca-Cola, McDonald's and VISA, as well as on an individual basis through continued conversations with the organization, AB InBev said in a statement on Friday.
Blatter said he will not resign as it would not be in the best interest of the organization. Visa and Adidas did not immediately respond to CNBC's requests for comment.
The calls come amid probes by the U.S. Department of Justice and the Swiss Attorney General's Office into corruption at FIFA after the indictment of 14 senior soccer officials and sports marketing executives in May.
Last month, FIFA put its second-ranking official, Jerome Valcke, on leave after an ex-footballer raised allegations he was involved in a plan to resell 2014 World Cup tickets for a lucrative profit.
—Reuters contributed to this report.