This research explores a novel encapsulating agent for establishing a synbiotic relationship with Bacillus (B.) coagulans by combining different ratios of wall materials, including skim milk powder (S), maltodextrin (M), and cellulose acetate phthalate (C). The ratio options are represented as SMC1 (1:2:1), SMC3 (3:2:1), SMC5 (5:2:1), and SMC7 (7:2:1). These wall materials are incorporated with 5% inulin (a prebiotic). The results show that these agents effectively protect B. coagulans spores during spray-drying, resulting in spore vitality exceeding 6 log cfu/g; SMC5 and SMC7 yielded the highest spore viability values. Furthermore, SMC5 demonstrated the highest levels of antioxidant activity, encompassing the scavenging of DPPH, hydroxy radicals, and superoxide radicals. Additionally, it displayed notable antidiabetic effects, including inhibitions of α-amylase and α-glucosidase. In comparison, SMC7 exhibited the most potent antidiabetic activity by inhibiting DPP-IV. Subsequently, after simulated gastrointestinal digestion, SMC5 and SMC7 showed a slight decrease in spore viability during the 6-hour simulation. Therefore, the most suitable condition for synbiotic production was found to be SMC5, which can potentially protect B. coagulans spores and exhibit bioactive activities after microencapsulation and passage through gastrointestinal digestion. This innovative product can be utilized as an advanced food delivery system and as a functional ingredient in functional food products.