The new recipes include the Spongebob Squarepants, Halloween and winter shapes. Two new shapes will also be added.
The change doesn't affect Kraft's traditional elbow-shaped macaroni and cheese with so-called "original flavor."
The change comes as consumers demand more natural foods. The packaged food company said the changes are not a result of an online petition. The petition, posted in March, had more than 348,000 signatures on Thursday.
The Associated Press contributed to this report.