The ethanolic extracts of habanero pepper contain two main groups of bioactive compounds: carotenoids, responsible for its characteristic color, and capsaicinoids, which give it its pungency. However, these compounds are sensitive to heat and oxidation, leading to their degradation over time. An alternative to protect these valuable compounds is the microencapsulation. This process involves using biopolymers to create a protective wall around the bioactive components, through of techniques like spray drying. The temperature and relative humidity are considered essential factors for preserving the integrity of the bioactive compounds during storage. Then, the objective of this research was to determine the critical storage conditions for the microcapsules. In this study, maltodextrin (MD) and a mixture with precipitated silica in a 95:5 w/w ratio (MDSP) were used as wall materials, and the spray drying was coupled with a heat pump in a closed loop configuration. The water adsorption isotherms and glass transition temperature were used to construct state diagrams (SD) using various mathematical models. The monolayer values, which indicate the point of maximum stability, were found in 6.17 and 6.76 g of water/100 g d.s. for MD and MDSP, respectively. The SD revealed critical water activity values (a_WC) of 0.49 for MD and 0.41 for MDSP. When both samples were stored at aw>0.4 (a_WC) the samples underwent physical transformations and, in addition, exhibited the greatest total color change, ΔE > 8. While those stored below a_WC, presented the smallest change, ΔE<4, consistent with the state diagrams.