Polymer microcapsules can be used as controlled release systems in drugs or in foods. Using layer-by-layer adsorption of common food proteins and polysaccharides, we produced a new type of microcapsule with tunable strength and permeability. The shell consists of alternating layers of pectin and whey protein fibrils, yielding a fiber-reinforced nanocomposite shell. The strength can be tightly controlled by varying the number of layers or the density and length of the fibrils in the protein layers. The mechanical stability of these microcapsules appears to be superior to that of currently available multilayer capsules. The method involves only standard unit operations and has the potential for scaling up to industrial production volumes.