Carotenoids are bioactive compounds that can be found in different food matrices. However, these compounds are easily degradable at high temperatures, light and oxygen. Therefore, it is necessary to search for an alternative that avoids such deterioration. Objective: The present study aimed at evaluating the storage stability of microencapsulated palm (Elaeis guineensis) and urucum (Bixa orellana) oil carotenoids by spray drying, depending on the composition of the encapsulation matrix. Methodology: a comparison was made between two types of formulations, a layer composed of isolated soy protein and a double layer composed of isolated soy protein and pectin. The procedure was split into three stages: 1) formulation of stable emulsions; 2) spray drying and 3) characterization of the microcapsules by evaluation of parameters such as encapsulation efficiency, color, humidity and stability of carotenoids over a period of 45 days. Conclusion: the addition of pectin as a double-layer encapsulation material is favorable for all the evaluated parameters except humidity, for which it was not possible to analyze its response during drying