Wrinkled microcapsules have attracted great interest due to their distinguished features, including enhanced adhesion propensity and release profiles. These features could be beneficial for food-related applications and improve the bioavailability of encapsulated compounds by promoting their attachment to epithelium. However, the fabrication of such microcapsules with food-grade materials has been met with limited success. In this study, a facile approach to produce wrinkled microcapsules using a food-grade protein, zein, is proposed. Internal phase separation was used to form zein microcapsules and three acids (phytic acid, citric acid, and succinic acid) were incorporated at two concentration levels (10 mM and 20 mM) to modify the secondary structure of zein in the microcapsules. The results showed that the mechanical properties of the microcapsules, which were characterized by nanoindentation, were greatly dependent on the protein secondary structure, particularly the a helix structure. The morphology of the microcapsules was evaluated by image analysis. An extensive wrinkle was observed on the surfaces of the microcapsules with high viscoplasticity. Among the three acids used in this study, phytic acid significantly increased the degree of wrinkling and viscoplasticity of the microcapsules. Further characterization with circular dichroism and wide-angle X-ray scattering suggested that a less ordered zein secondary structure was formed in the samples prepared using phytic acid than in those prepared using other acids or without acid, which further supports the hypothesis that the nanomechanical properties and degree of wrinkling are associated with the protein secondary structures.