Living probiotics secrete bioactive substances to accelerate wound healing, but the clinical application of antibiotics inhibits the survival of probiotics. Inspired by the chelation of tannic acid and ferric ions, we developed a metal-phenolic self-assembly shielded probiotic (Lactobacillus reuteri, L. reuteri@FeTA) to prevent interference from antibiotics. Here, a superimposing layer was formed on the surface of L. reuteri to adsorb and inactivate antibiotics. These shielded probiotics were loaded into an injectable hydrogel (Gel/L@FeTA) formed by carboxylated chitosan and oxidized hyaluronan. The Gel/L@FeTA aided the survival of probiotics and supported the continuous secretion of lactic acid to perform biological functions in an environment containing gentamicin. Furthermore, the Gel/L@FeTA hydrogels presented a better performance than the Gel/L in inflammatory regulation, angiogenesis, and tissue regeneration both in vitro and in vivo in the presence of antibiotics. Hence, a new method for designing probiotic-based biomaterials for clinical wound management is provided.