The extensive range of applications where synthetic nanomaterials are nowadays used is causing a huge commercial market. An incipient use of these nanomaterials arises from the need to generate alternative antimicrobial agents, anticipating the development of resistant microorganisms. Here, we show a nanostructured ZnO with antimicrobial properties and low-cytotoxicity based on a nanoparticles arrangement by controlling the formation of sintering-neck into nanoporous spheres. The antimicrobial effectiveness of ZnO spheres is tested in a broad-spectrum of microorganisms such as fungi, Gram-negative and Gram-positive bacteria. The hierarchical structures show highly effective antimicrobial activity at low concentrations and in relatively short action times (24-72h). We demonstrate that the enhanced antimicrobial properties against microorganisms are ascribed to a combining of both physical and chemical interactions between microorganism and ZnO. The approximation mechanism between microorganism and ZnO is provided through electrostatic forces (physical interaction) which, thanks to the ZnO-microorganism proximity, promote a rapid release of zinc cations and the reactive oxygen species penetration into microorganisms (chemical interaction). We believe that this work provides insights on the mechanisms underlying the interactions ZnOmicroorganism and possess a combined action mechanism for which nanostructured ZnO is so effective to combat microorganisms.