In recent years, infections and the escalating resistance to antimicrobial drugs have emerged as significant health concerns. Due to their remarkable effectiveness and minimal potential for bacteria to develop resistance, copper-based nanomaterials are being considered as prospective alternatives to conventional antibiotics. In this study, copper pyrophosphate nanoflakes were synthesized using a simple hydrothermal technique with an inorganic phosphate source. These nanoflakes, characterized by a high aspect ratio, exert a substantial impact on bacterial cell walls, effectively eliminating microbial pathogens. X-ray diffraction (XRD) analysis confirmed the monoclinic phase of the copper pyrophosphate nanomaterial, while the band gap energy of 2.7 eV was estimated from the Tauc plot. Additionally, the antimicrobial efficacy of Cu2P2O7 was evaluated against various gram-negative, gram-positive, and fungal pathogens at different concentrations. Notably, all tested bacterial strains exhibited moderate antimicrobial effects at concentrations of 5 mg/mL. For instance, S. aureus and E. coli displayed a 13 mm zone of inhibition, demonstrating excellent activity and lower cytotoxicity. These findings underscore the potential of Cu2P2O7 as a promising candidate for the development of novel drugs targeting pathogenic bacteria affecting human health.