This study aims to investigate physical stability and antioxidant properties of spray-dried red (Hylocereus polyrhizus) and white (Hylocereus undatus) dragon fruit powder upon storage at various relative humidity (RH). Inlet air temperatures of 120 °C (red dragon fruit) and 110 °C (white dragon fruit) as well as maltodextrin concentration of 30% (w/v) were selected as the spray drying conditions as powder was obtained at these minimum conditions. The powder was ranging from 3 to 7 μm in particle size with spherical morphology. The powder had lower antioxidant content and antioxidant activities compared with the control before spray drying. Storage of powder at 43%, 54% or 75% RH at 25 °C for 25 days resulted in structural changes correlating to the depression of glass transition temperatures (Tg) to below storage temperature. At 33% RH, no visible structural changes were observed. Antioxidant properties of the powder remained unchanged after 25 days' storage at the studied RHs.