Objective Although organic-inorganic hybrid nanoflowers (hNFs) with much enhanced catalytic activity and stability were fabricated using proteins and enzymes, in this study, for the first time, we report synthesis of allicin and copper ion (Cu2+) coordinated NFs and investigate their peroxidase-like and antimicrobial activities. Results The allicin (active ingredient of Allium sativum) and Cu2+ was acted as an organic and inorganic part, respectively for synthesis of the Cu-hNFs. The hNFs were characterized by various techniques. Spherical, uniform, mono-dispersed and flower-like-shaped morphology of the hNFs (synthesized at pH 5) were imaged by scanning electron microscopy. The presence of Cu metal in the hNFs was detected by energy dispersive X-ray spectroscopy. Characteristic bonds stretching and bending for structural analysis of the hNFs were carried out by Fourier transform infrared spectrometry. In terms of applications, the hNFs showed quite effective peroxidase-like activity towards to guaiacol (used as a model substrate) in the presence of hydrogen peroxide (H2O2) through Fenton reaction. We demonstrated that the NFs exhibited similar to 200% and similar to 500% higher catalytic activities in 1 h (hr) and 3 h (hrs) than their initial catalytic activity measured in 5 minute (min). Additionally, effective antibacterial properties of the Cu-hNFs were observed against fish pathogen bacteria (Aeromonas hydrophila, Vibrio parahaemolyticus, and Lactococcus garvieae). Conclusions We finally demonsrated that allicin based hybrid nanomaterial can be prepared by a relatively cheap, one step, easy and eco-friendly method. The allicin hNFs can be considered as novel Fenton agent for peroxidase like activity and bactericidal.