Zinc oxide nanoparticles (NPs) with the size of similar to 100 nm were prepared via a facile biomineralization process in the template of silk fibroin (SF) peptide at room temperature. These ZnO NPs have shown the remarkable behavior of low toxicity to Gram-positive bacteria (Staphylococcus aureus, Staphylococcus agalactiae), Gram-negative bacteria (Escherichia coli), and eukaryotic cells (mouse L929 fibroblasts). Bacteriological testing indicated that ZnO NPs presented a 50% inhibitory effect on Streptococcus agalactiae at the concentrations of >100 mM, whereas at the same concentrations, the growth of Staphylococcus aureus and Escherichia colt were hardly inhibited. On the other hand, a remarkable proliferation of Staphylococcus aureus or Escherichia coli was observed at the concentrations of ZnO NPs <50 mM. Moreover, the cytotoxicity test demonstrated that ZnO NPs mineralized with SF peptide possessed a low toxicity to mouse L929 fibroblasts. The SF peptide coated on the surface of ZnO NPs permitted greater adhesion and consequently greater proliferation of mouse L929 fibroblasts. Besides, from TEM micrographs of the cell ultrastructure, endocytosis of NPs into the cytoplasm can be detected and the ultrastructure of the cell underwent few changes. The cell membrane retained integrity, euchromatin dispersed homogenously inside the cytoplasm, the mitochondrial architecture remained intact, and no intracellular vacuoles were observed. High-resolution transmission electron microscopy images and selected area electron diffraction patterns of ultrathin cell sections indicated that the crystal structure of NPs was not damaged by the organelle or cytoplasm. All these observations indicated that ZnO NPs mineralized with the SF peptide possess good cytocompatibility.