<p>This study investigates a hybrid clinoptilolite–skim milk powder (SMP) matrix for the stabilization of <i>Bifidobacterium bifidum</i> under freeze- and vacuum-drying. Structure–property relationships were evaluated by correlating microstructural features with microbial viability. Field-emission scanning electron microscopy (FE-SEM) and particle size distribution (PSD) revealed more compact and integrated structures in hybrid systems than single-component carriers. Brunauer–Emmett–Teller (BET) analysis revealed substantially higher surface areas in clinoptilolite-containing matrices (~ 10–12 m²/g) than in hybrid formulations (~ 1–2 m²/g), suggesting partial surface coverage of clinoptilolite by milk components. Fourier transform infrared (FTIR) spectroscopy confirmed the integrity of protein secondary structures (Amide I and II) and the zeolite framework post-dehydration. Freeze-drying preserved <i>B. bifidum</i> viability more effectively than vacuum drying across all carrier systems. Clinoptilolite-containing systems exhibited lower residual moisture compared to milk-based matrices; however, reduced moisture alone did not ensure improved viability. During 90-day storage, freeze-dried SMP and hybrid formulations showed the highest viability, retaining 8.60 and 8.56 log CFU/g, respectively, whereas zeolite-only systems exhibited substantial viability losses. The results indicate that probiotic stability is influenced by matrix–process interactions, highlighting the role of clinoptilolite in moisture modulation and its contribution to the physicochemical characteristics of hybrid systems.</p> Graphical abstract <p></p>