SD LGG formulation with [HWP (or WPI)–DGS–RS–oil matrix] also offered the best protection to probiotics under accelerated storage conditions at 40 °C × 75% RH in aluminium foil packaging and at elevated RH environment (32, 57, 70% RH), although long term storage stability was not achieved. This study provided new insights regarding the importance of encapsulant matrix formulation, in combination with appropriate packaging and storage temperature condition, to achieve long term stability of spray dried LGG microcapsules. These also provide an opportunity to develop a much wider range of non-refrigerated functional food formulations as delivery vehicle for probiotics.