Ensuring healthy lives and promoting well-being for all at all ages is the third goal of the sustainable development plan, so it was necessary to identify the most important problems that threaten health in our world. The World Health Organization declared that antibiotic resistance is one of the uppermost global public health threats facing humanity and searching for new antibiotics is slow. This problem can be approached by improving available drugs to combat various bacterial threats. To circumvent bacterial resistance, three copper(II) complexes based on the pefloxacin drug were prepared and characterized using analytical, spectroscopic, and thermal techniques. The resulting data suggested the formation of one octahedral binary and two distorted square pyramidal ternary complexes. Fluorescence spectra results revealed the formation of a turn-on fluorophore for amino acid detection. Computational calculations investigated quantum and reactivity parameters. Molecular electrostatic potential profiles and noncovalent bond interaction-reduced density gradient analysis indicated the active sites on the complex surface. The complexes were subjected to six microbial species, where the octahedral binary complex provoked its antimicrobial potency in comparison with ternary complexes. The enhanced antimicrobial activity against gram-negative bacteriumE-colicompared to gentamicin was exhibited by the three complexes. Docking simulation was performed based on the crystal structure ofE. coliandS. pneumoniaereceptors using 5I2D and 6O15 codes. The binary complex exhibited a potent fitness score with 5I2D (TBE = − 107 kcal/mol) while ternary complexes displayed the highest docked score of fitness with 6O15.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13065-023-00962-x.