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 Levilactobacillus brevis 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.