We demonstrate the assembly of extremely robust and pH-responsive thin shell LbL microcapsules from silk fibroin counterparts modified with poly(lysine) and poly(glutamic) acid, which are based on biocompatible silk ionomer materials in contrast with usually exploited synthetic polyelectrolytes. The microcapsules are extremely stable in an unusually wide pH range from 1.5 to 12.0 and show a remarkable degree of reversible swelling/deswelling response in dimensions, as exposed to extreme acidic and basic conditions. These changes are accompanied by reversible variations in shell permeability that can be utilized for pH-controlled loading and unloading of large macromolecules. Finally, we confirmed that these shells can be utilized to encapsulate yeast cells with a viability rate much higher than that for traditional synthetic polyelectrolytes.