The influence of spray drier inlet (180 and 200 °C) and outlet (80, 90 and 100 °C) air temperatures and storage parameters (22 and 40 °C, and 11%, 23% and 54% RH, for 6 months) on the characteristics of infant milk formula (IMF) powders was investigated. The combination of inlet–outlet temperatures affected the moisture content, water activity, particle size and glass transition temperature (Tg) in the freshly spray-dried IMF powders, whereas, powder surface composition and morphology were not affected. Powders remained stable for 6 months at 11 and 23% RH at both storage temperatures. Storage at 54% RH (at both storage temperatures) increased the moisture uptake by powders, decreased Tg below storage temperature, induced lactose crystallisation, increased surface fat and caking of powders, and reduced powder solubility. This study shows that inlet–outlet temperature combinations used during spray drying affect the stability of powders during storage by affecting their initial moisture content.