Display omitted •Chiral L/D-BDP NPs with antibacterial activity, were prepared and characterized.•L-BDP NPs exhibited higher photodynamic antibacterial activity against S. aureus.•2% LCG film had excellent photodynamic bactericidal effect.•2% LCG film could protect the packaged cherries against microorganisms.•2% LCG film could effectively extend the shelf life of packaged cherries. The concept of transferring the chirality from small molecules to nanomaterials has aroused great interest. On the other hand, photodynamic inactivation (PDI) is a promising technology for food preservation, due to its high antibacterial ability and none microbial resistance. Herein, chiral boron dipyrromethenes (denoted as L/D-BDP) were prepared and their nano-formulations (L/D-BDP NPs) were fabricated. L/D-BDP NPs significantly amplified the chirality of L/D-BDP, leading to essentially enhanced antibacterial activity. L/D-BDP NPs could eradicate Gram-positive bacteria (S. aureus), with L-BDP NPs showing more significant antimicrobial activity than D-BDP NPs. Different content (0, 0.5%, 1% and 2%) of L/D-BDP NPs were doped with chitosan and glycerol to prepare antibacterial films (CG, 0.5%L/DCG, 1%L/DCG and 2%L/DCG, respectively). Among which, 2%LCG film has the most efficacious antimicrobial activity. In the 8-day cherry preservation experiment, 2%LCG film irradiated with green light for 8 min could effectively inhibit cherries mildew, delay the loss of vitamin C and total polyphenol content, and significantly prolong the storage period of cherries at room temperature. This study presents a new approach for constructing highly efficient chiral antimicrobial nano-agents, which is conducive to develop chiral functional nanomaterials that tailored for specific biological and medical purposes.