The aim of the work was to investigate the effect of different packaging materials and storage temperatures on the stability and in vitro properties of microencapsulated spray-dried synbiotic kidney-mung bean beverage (KMB) powder. The formulation for the synbiotic KMB powder has been explored in our previous work. The present study focuses on the evaluation of the shelf-life of the same synbiotic KMB powder. The synbiotic powder was packed in polypropylene and aluminum laminates and stored at 25, 30, and 35 °C. The survivability of probiotic Lacticaseibacillus casei in encapsulated spray-dried powder was studied under simulated gastric conditions for 70 days. At all three storage temperatures, the count remained >108 CFU mL−1 for the first 21 days. Additionally, moisture content increased and color value (L*) decreased with increasing storage time, irrespective of packaging material. The encapsulated synbiotic powder in Al-laminate pouches also showed better prebiotic activity when compared to PP laminates. An acceptable sensory score (6 out of 10) and low microbial load (<106 CFU mL−1) also suggested that the shelf life of synbiotic KMB powder in polypropylene and aluminum laminates was 63, 35, and 35 days at 25, 30, and 35 °C, respectively.