<p>The antibacterial characteristics of nanoparticles serve as a crucial factor in combating infections, whereas their textural properties determine their interaction with biological systems. In this study, zinc stannate nanostructures, such as nanocubes, nanoplatelets, nanoparticles, nanorods, and polyhedrals, were synthesized by an economic hydrothermal approach and were morphologically and structurally characterized by transmission electron microscopy, field emission scanning electron microscopy (FE-SEM), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, and X-ray diffraction (XRD). The adsorption-desorption isotherms indicated a substantially high Brunauer-Emmett-Teller (BET) surface area of 91.995 m²g^− 1 for nanoparticles and 45.259 m²g^− 1 for the polyhedral morphology of zinc stannate. All the obtained morphologies for zinc stannate are considered as mesoporous materials, as concluded from Barrett-Joyner-Halenda (BJH) pore size distribution. The minimum inhibitory concentration (MIC) value for these nanostructures was determined against Gram-negative (<i>E. coli)</i> and Gram-positive (<i>S. aureus)</i> bacteria. The lowest MIC values of 4&#xa0;mg/L and 8&#xa0;mg/L were recorded for nanorods and nanoparticles, respectively, against <i>E. coli</i>, while the highest MIC value of 2048&#xa0;mg/L was recorded for polyhedra morphology against <i>S. aureus</i> bacteria. The observations obtained from the time-kill assay in terms of optical density of bacteria at 600&#xa0;nm (OD₆₀₀) are in synchronization with MIC value calculations and showed a good correlation with the fitted dose-response curve, with an R² value of 0.993. The present investigation has shown that the antibacterial activity of zinc stannate nanostructures is significantly influenced by their crystal phase and morphology-related characteristics, including surface area, pore volume, and pore size distribution.</p> Graphical Abstract <p></p>