The yellow color of Cheddar cheese whey is due to the presence of annatto, which partitions into the whey during the Cheddar cheese making process. Currently, bleaching of the color using strong oxidizing agents such as hydrogen peroxide or benzoyl peroxide brings up the challenges such as health issues for asthmatic people, generation of off-flavors as a result of lipid oxidation, and loss of nutritive value due to whey protein oxidation. As the global market for whey protein is projected to reach 13.5 billion dollars by 2020, providing an appropriate method to obtain high quality whey from the colored Cheddar cheese process to avoid challenges associated with current bleaching processes is of significant importance. The objective of this study is to selectively add colorant to cheddar cheese and prevent partitioning of color into whey. In this work we design a controlled-release platform to selectively deliver and release annatto within cheddar cheese matrix. We encapsulate annatto within a protein-polysaccharide complex shell using emulsification followed by spray drying steps (42% encapsulation efficiency). The engineered shell material disintegrates by the enzymes secreted during the ripening period of cheddar cheese and releases the encapsulated annatto into the cheddar cheese matrix. The Hunter CIE Lab color analysis shows an increase in the yellowness (b* value) of the cheese during the ripening period of 1 mo. Exploiting this method, we produce colored cheddar cheese and white cheddar cheese whey without any need to discolor whey. This enzymatically-triggered microcapsule design posses a great potential to be commercialized and utilized worldwide to enhance the quality of both cheddar cheese and its recovered whey.