Robust and stable microcapsules are assembled from poly-amino acid-modified silk fibroin reinforced with graphene oxide flakes using layer-by-layer (LbL) assembly, based on biocompatible natural protein and carbon nanosheets. The composite microcapsules are extremely stable in acidic (pH 2.0) and basic (pH 11.5) conditions, accompanied with pH-triggered permeability, which facilitates the controllable encapsulation and release of macromolecules. Furthermore, the graphene oxide incorporated into ultrathin LbL shells induces greatly reinforced mechanical properties, with an elastic modulus which is two orders of magnitude higher than the typical values of original silk LbL shells and shows a significant, three-fold reduction in pore size. Such strong nanocomposite microcapsules can provide solid protection of encapsulated cargo under harsh conditions, indicating a promising candidate with controllable loading/unloading for drug delivery, reinforcement, and bioengineering applications.