ABSTRACT The in vivo functionality of oral probiotics is often compromised by their susceptibility to environmental and gastrointestinal stressors, coupled with limited mucosal retention. To overcome these challenges, we developed a smart, pH‐responsive biomaterial platform based on shellac microgels (SCM), derived from a natural, biocompatible insect resin. Combining experimental characterization with finite element analysis, we verified that the densified molecular network of SCM functions as a potent physical barrier that effectively hinders the diffusion of O 2 , moisture, and UV radiation, as well as physiological assaults (H + and bile salts), protecting the viability of probiotics throughout storage and gastrointestinal transit. Crucially, the pK a ‐dependent phase transition of SCM enabled precise colon‐targeted bio‐interface, where its abundant functional groups facilitated strong mucosal anchoring via non‐covalent interactions. In a DSS‐induced colitis mouse model, this precision‐release strategy significantly improved therapeutic outcomes by suppressing the inflammation, restoring gut homeostasis, and repairing the epithelial barrier. This study presents a sustainable, potent, and naturally derived biomaterial strategy for the controlled delivery of sensitive bacterial therapeutics.