In this study, the effectiveness of microencapsulation using maltodextrin (MD) and γ-polyglutamic acid (γ-PGA) in enhancing the survival of probiotic Bifidobacterium bifidum (ATCC 29521) against simulated gastrointestinal fluids and under different storage conditions, was investigated. By using 1.0% γ-PGA + 20% MD in encapsulation, the tolerance of B. bifidum to simulated gastric and intestinal fluids was significantly improved. This combination also showed enhanced stability over three weeks of storage at 4 °C and 25 °C. Size distribution analysis revealed that higher γ-PGA content resulted in smaller micro-flakes (<100 µm). Scanning electron microscopy demonstrated that encapsulation with 20% MD + 0.5% or 1.0% γ-PGA created smoother, less porous surfaces than that with MD alone. X-ray photoelectron spectroscopy further showed that incorporation of γ-PGA increased the carboxylic acid content, suggesting stronger chemical bond interactions between the bacterial membrane and the composites. Overall, these results indicate that freeze-dried probiotic B. bifidum prepared using 20% MD and 1.0% γ-PGA can be stored in powdered form and is highly resistant to simulated gastrointestinal fluids, making the composite an ideal food-grade protective biopolymer.