Probiotic oral delivery is challenged by harsh gastrointestinal conditions and environmental stressors in the body. This study presents the construction of durable nanoshells composed of an Fe³⁺-phytic acid metal-organic complex around individual probiotic cells, providing exceptional cytoprotective properties, in single-cell nanoencapsulation. Nanoencapsulated <i>Levilactobacillus brevis</i> maintains high viability under simulated gastric fluid and the antibiotic tetracycline. The Fe³⁺-phytic acid nanoshells provide an effective platform for improving the viability and functionality of probiotics in therapeutic and nutritional applications.