The objective was to evaluate the effect of glass transition on chemical properties, caking, and flowability of soymilk powder during storage. Samples were stored for 18 weeks under different water activities (Aw: 0.328–0.902) and temperatures (T: 10–55 °C). Chemical changes (antioxidant capacity, phenolic compounds content, and color) and powder flow properties were evaluated using dynamic rheological measurements of the amorphous powder at glassy and rubbery states. The results showed that chemical changes occurred during storage as an effect of Aw and temperature. However, the physical state (glassy × rubbery) had a more relevant role in the degradation of the components. The flow properties of the soymilk powder showed that cohesion, as well as the normalized basic flow energy (NBFE), can be correlated to the rubbery state. The temperature showed higher NBFE values when sample was stored in rubbery state. The results can help understand the role of glass transition on soymilk powder stability.