An orthogonal polymerization reaction between two monomers partitioned in the two liquid phases of a miniemulsion yielded nanocapsules with various functional groups (sulfonate, amine, carboxylic acid, and poly(ethylene glycol) (PEG). The formation of the nanocapsules could be realized in the presence of a self-healing agent in the liquid core. We present here the conditions for the successful preparation of functional polymer nanocapsules by free-radical polymerization as orthogonal reaction for self-healing materials. The stability of the nanocapsules was assessed by AFM measurements in the dried state as well as in water.