•A facile strategy was developed to fabricate functional starch Zn(II)@l-Phe-g-St.•The structure of Zn(II)@l-Phe-g-St was proposed and well characterized.•Zn(II)@l-Phe-g-St had good antibacterial activity against B. subtilis and E. coli.•Zn(II)@l-Phe-g-St was found to be very low toxicity.A facile strategy was developed to fabricate zinc (II) functionalized l-phenylalanine in situ grafted starch (Zn(II)@l-Phe-g-St). The structure of Zn(II)@l-Phe-g-St was proposed and well characterized, and the assays of antibacterial activity against typical bacteria (Bacillus subtilis and Escherichia coli) and cytotoxicity of Hela cell were focused on. Boc-l-phenylalanine was used to achieve l-Phe-g-St by in situ grafting onto starch through esterification reaction after removal of Boc. It was confirmed that around 71.02% of NH2 of l-Phe complexed with Zn(II) by σ-coordinate bonds and the coordination number of Zn(II) approximated to 2. Zn(II)@l-Phe-g-St exhibited a good antibacterial activity against both Bacillus subtilis and Escherichia coli with increasing its concentration, and a relatively more effective antibacterial activity against Bacillus subtilis than Escherichia coli. Furthermore, Zn(II)@l-Phe-g-St was found to be very low toxicity towards Hela cells especially at the concentration below 40 μg ml−1.