Bioactive agents play a pivotal role in determining the function and performance of biomedical products and devices across tissue engineering, regenerative medicine, and cosmetic applications. Silk fibroin (SF) is an extensively used structural biomaterial, yet its inherent bioactive potential remains unexplored for material design. In this study, we developed β-sheet-rich silk nanofiber aggregates (BSNFs) with controlled diameters at ∼20 nm through structural bioinspiration from native silk fibers. We systematically compared our engineered BSNFs to two other distinct forms, conventional amorphous SF solution (ASF) and recombinant silk protein (RSF), to reveal the influence of the material conformation and nanostructure on their bioactivity. Notably, while ASF demonstrated better in vitro antioxidant capacity, both BSNFs and RSFs exhibited enhanced cellular antioxidant activity through improved phagocytic uptake. The nanofibrous structure coupled with β-sheet-rich conformation facilitated cellular internalization and, thus, enhanced intracellular bioactivity. BSNFs outperformed ASF and RSF in stimulating cellular proliferation and migration, and they have better anti-inflammatory effects. Remarkably, BSNFs showed exceptional skin barrier protection capability and versatile activities in tissue repair and transepidermal delivery applications. This work establishes a paradigm shift by redefining SF aggregates as inherently bioactive components with their distinct nanostructures serving as critical activity modulators. Our findings not only reinforce silk's value beyond structural applications but also provide a rational design for developing next-generation functional silk biomaterials with enhanced bioactivities.