A novel biocompatible shell-crosslinked nanocapsule system was developed based on nanoemulsion templates stabilized by a class of food proteins. The nanoemulsion templates were prepared using a combination of mechanical mixing and high-pressure homogenization, while the nanocapsule shell formed simultaneously through calcium ions-induced crosslinking of the food proteins. These core–shell structured nanocapsules with a particle size of about 200 nm showed high drug-loading capacity and well improved stability in comparison with their nanoemulsion counterpart. The nanocapsule suspension can be freeze-fried directly; and the solidified nanocapsules can be well reconstituted in water, retaining their original particle size. It is concluded that the nanoemulsion-templated core–shell structured nanocapsules can be used as novel drug delivery systems with high loading capacity for poorly water-soluble drugs as well as well improved long-term and storage stability. Furthermore, the presence of surface food proteins introduces carboxyl and amine moieties, which enables the nanocapsules to anchor ligands, suggesting its potential application in targeting drug delivery, bioimaging and therapeutics.