But the initiative quickly raised hackles from dietitians and public-health advocates who said it marred the academy's reputation as a nutritional advocate immune to influence from the food industry.
"Although we stand by our decision to work together to shine a light on this issue, and not to serve as a product endorsement, we believe misperceptions are overshadowing the campaign," said Kraft spokeswoman Jody Moore.
"As such, both organizations have agreed it is best not to proceed as originally planned."
Moore said the labels would continue to appear on Kraft Singles through approximately July.
A March 16 petition signed by members of the dietitians group called on the academy to end the collaboration, saying the venture "has put our professional integrity and credibility at risk."
The petition also called on the academy to disclose financial terms between the foundation and Kraft.
An academy spokesman said the group had no comment.
Copyright Agence France-Presse, 2015