© 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.First time in this study, organic@inorganic hybrid copper nanoflowers (Cu NFs) were synthesized by using cherry stem extract as an organic component and Cu2+ ion as an inorganic component. For this purpose, cherry stalk extracts were obtained by using ethanol and water solvents. Cu NFs were synthesized in different amounts of extract (100–1000 µl) and under various pH (7.4–9) conditions. The morphologies of the synthesized Cu NFs were evaluated by field emission scanning electron microscope (FE-SEM). The functional groups in the cherry stem extract, which play an active role for the synthesis process, and the crystal structure of NFs were investigated by Fourier transform ınfrared spectroscopy and X-ray diffraction techniques, respectively. It has been determined by the FE-SEM analysis that ethanol and water based cherry stem extracts are suitable for Cu NFs synthesis in a wide range of pH (7.4–9). This data is crucial for overcoming important limitations for NF synthesis, such as narrow-range medium pH. The catalytic, antioxidant, and antimicrobial activities of Cu NFs were evaluated. It was revealed that Cu NFs have catalytic, antioxidant, and antimicrobial activities. It is recommended that, cherry stem extract and different inorganic components are functional to synthesize numerous NFs and to evaluate the adequacy of use in biomedical fields.