We studied the pH-responsive behavior of layer-by-layer (LbL) microcapsules fabricated from silk fibroin chemically modified with different poly amino acid side chains: cationic (silk-poly L-lysine, SF-PL) or anionic (silk-poly-L-glutamic acid, SF-PG). We observed that stable ultrathin shell microcapsules can be assembled with a dramatic increase in swelling, thickness, and microroughness at extremely acidic (pH < 2.5) and basic (pH > 11.0) conditions without noticeable disintegration. These changes are accompanied by dramatic changes in shell permeability with a 2 orders of magnitude increase in the diffusion coefficient. Moreover, the silk ionomer shells undergo remarkable softening with a drop in Young's modulus by more than 1 order of magnitude due to the swelling, stretching, and increase in material porosity. The ability to control permeability and mechanical properties over a wide range for the silk-based microcapsules, with distinguishing stability under harsh environmental conditions, provides an important system for controlled loading and release and applications in bioengineering.