Protein nanocapsules are potentially useful as functional nanocarriers because of their hollow structure and high biocompatibility and the intrinsic activity of their protein constituents. However, the development of a facile method for the preparation of oriented nanocapsules that retain their protein activity has been challenging. Here we describe the preparation of protein nanocapsules through the enzymatic removal of polymer templates. Nickel(II) nitrilotriacetic acid-end-functionalized poly(lactic acid) (Ni2+-NTA-PLA) was introduced as a polymeric template to immobilize hexa-histidine-tagged green fluorescence protein (His6-GFP) with consistent orientation. Following protein cross-linking and core-degradation, various measurements as a function of degradation time indicated the formation of hollow structures. We also demonstrated orientational control and activity preservation of the protein after capsule preparation. Protein nanocapsules prepared by this method can act as functional containers, taking advantage of the intrinsic function of their constituent proteins without additional modification.