Pefloxacin-based mixed ligand Cu(II) complexes with substituted isatin of type [Cu(Isatin)(Pefloxacin)Cl] were synthesized, and characterized by EPR, mass, FT-IR, electronic spectrometry, metal content, magnetic moment, and conductance measurement. The g factors g ∥ > g ⟂ > 2.0023 observed in EPR suggest a square-pyramidal environment of ligands around the copper metal. The compounds were screened for diverse biological activities. The compounds inhibit efficiently the cell proliferation of HCT 116 cancer cells. To take the insight of anticancer activity mechanism, we investigated compound-1 for further cellular assay-based biological activities like trypan blue assay, cell morphological alteration assay, colony formation assay, cell apoptosis, and cell necrosis assay. The compound-1 induced distinct morphological alteration in cells, inhibits cell viability, decreases % plating efficiency, and decreases the clonogenic ability of the HCT 116 cells. The cell death mechanism was confirmed by annexin V-FITC / PI assay and LDH release assay. The positive annexin V/PI stained cells in presence of compound-1 and the absence of a significant amount of lactate dehydrogenase suggest cell apoptosis mechanism for anticancer activity of compounds. We also screened compounds for in vitro antibacterial and cytotoxic activities.