Aqueous microdroplets introduced in ionic liquids (ILs) provide unique interfaces where surface-modified protein microcapsules are spontaneously formed at systemic temperature. The susceptibility of proteins to form microcapsules at the water-IL microinterface depends on protein species and is related to the number of charged residues exhibited on protein surfaces. When both of the capsule-forming (host) proteins and guests biopolymers such as nucleic acids or enzymes are introduced in the aqueous microdroplets, microcapsules are formed selectively from host proteins while the guest biopolymers remain encapsulated in the aqueous pool. Microcapsules formed in the IL phase are facilely extracted to aqueous phase after consecutive cross-linking and surface modification reactions, and the whole processes can be done in one pot. Enzymes confined in the inner water phase of aqueous protein microcapsules showed innate activity, as visualized by site-specific fluorescence detection using confocal laser scanning microscopy (CLSM). The present IL-water interfacial synthesis of protein microcapsules eliminates the use of volatile organic solvents or solid colloid templates, which creates a much-coveted solution to existing technologies.