Due to the biological importance of carotenoids, several works have been developed aiming for the reduction of carotenoid degradation, and one notable proposed alternative has been the formation of microcapsules. Therefore, the aim of the current paper was the microencapsulation of carotenogenic extracts from Rhodotorula mucilaginosa and Sporidiobolus pararoseus by a lyophilization method utilizing gum arabic, xanthan gum, sodium alginate and soy protein-like wall materials. The gum arabic showed the greatest efficiency of encapsulation for the R. mucilaginosa (66.3±0.8 %) and S. pararoseus (91.4±0.9 %) carotenogenic extracts, while the soy protein showed the lowest efficiency of encapsulation (40.7±1.1 % for R. mucilaginosa and 68.5±1.5 % for S. pararoseus). Scanning electron micrographs (SEM) showed irregular structure formation that was independent of the material utilized for the encapsulation. In this way, it was possible to observe that the wall materials directly affect the encapsulation efficiencies, morphology, and thermal behavior of the capsules of natural carotenoids.