Annatto is commonly used as a natural colourant in processed food products. Due to its chemical structure, it is sensitive to environmental factors such as oxygen, temperature and light. Carotenoid extraction using chemical methods requires greater expenditure of time and energy, leading to potential repercussions on the quality and safety of the end product. This study aims to encapsulate the Annatto extract (AE) produced using a developed extractor with different concentrations of maltodextrin (MD) and gum arabic (GA) used as carrier materials to improve the solubility and stability. The formulation 50:0 (MD: GA) showed a remarkable microencapsulation efficiency 86.28 ± 0.14 % with a process yield 195.75 ± 3.20 g/500 ml, bulk density 0.281 ± 0.012 g cm−3 and water activity of 0.65 ± 0.02. The AE microcapsules obtained good homogeneity and high solubility (>97 %) with a low moisture content of 4.07 ± 0.06 %. Furthermore, it was morphologically characterized as dodecahedron-shaped with a smooth surface and the absence of cracks or fissures offering complete protection to the bioactive compound encapsulated. The presence of bixin and polyphenol was confirmed by the FT-IR bands at 1646.91 cm−1, 1151.29 cm−1 and 926.26 cm−1. The purity was confirmed by the peaks drawn in the HPLC analysis. AE microcapsules were evaluated for heat stability up to 160 °C and storage stability for 60 days. Therefore, AE powders can be used as an alternative to synthetic additives which offer great potential as colorants in food matrixes.