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Herein we report a green method for the synthesis of organic-inorganic hybrid nanoflowers using a Trigonella foenum-graecum L. (TF) (Fenugreek seeds) extracts as an organic part and copper ions acting as an inorganic part. The organic-inorganic hybrid nanoflowers using TF seed extract (TF-Cu2+ hNFs) were characterized by SEM, XRD, EDX and FTIR. The morphology of the TF-Cu2+ hNFs was quite spherical and monodisperse with ∼18μm size. The TF-Cu2+ hNF exhibited the effective anti-bacterial activity against Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus, Bacillus cereus, Salmonella typhi and Escherichia coli at 1-10 µg ml-1 concentrations except against Pseudomonas aeruginosa and Haemophilus influenza. However, both TF-Cu2+ hNFs and free TF extracts showed any antifungal activities against Candida albicans or Candida glabrata. The study revealed that TF-Cu2+ hNFs could be used as a therapeutic agent for microbial infections and has the potential to overcome drug resistance.