Peru is the primary producer of annatto seeds (Bixa orellana L.). Annatto seeds are very attractive because they contain bixin as their main colorant, representing more than 80% of the pigments. Its aqueous extract could be encapsulated to improve quality conservation during transportation and storage time. Despite carotenoids could have polar character, in spray drying process, water is generally used to disperse active compounds and wall material. Therefore, the objective of this work was to microencapsulate annatto seed aqueous extract using a pilot scale spray dried at different maltodextrin – gum arabic ratios as wall material (MD:GA 100:0, 50:50, 0:100) and total solids concentration (20%, 30%, 40%). Finally, the stability of the best microparticles stored at 35 and 45°C was developed. The particles were evaluated according to humidity, encapsulation efficiency, color, density, solubility, phenolic compounds, carotenoids, ABTS, and DPPH. It was possible to obtain annatto microparticles as a high-added-value product. The highest value of encapsulation efficiency was obtained at 20% solids with MD:GA 50:50 (33.82%). In the color analysis, results for the a* and b* index indicate that treatments with 20% of total solids contain the highest values, reflecting these powders' higher bixin content. Carotenoid content indicates that this experiment (20% solid and MD:GA 50:50) presents the higher value (50595.42 ug β-carotene/g of powder), being this experiment, which storage analysis was made at 35 and 45 °C over four weeks. The carotenoid content of the microparticles was higher than that of annatto seeds throughout the analysis time. The microparticles protected these active compounds and were a good option to protect the concentrated carotenoids in the annatto aqueous extract. Furthermore, we can conclude that with an aqueous extraction, extracts rich in carotenoids can be obtained, which can then be microencapsulated.