Abstract Atmospheric pressure metal–organic chemical vapour deposition was used to synthesize Ag-containing ZnO nanostructures of different morphology on Si substrates coated by Ag. Ag from Ag/Si substrates and Ag from silver acetylacetonate after its decomposition were used as a catalyst for ZnO nanocrystal growth for deposition of ZnO nanostructures with different morphologies. We investigated the relation of the structural parameters and chemical composition probed by x-ray diffraction (XRD), x-ray photoelectron spectroscopy (XPS), and Raman spectroscopy with the photoluminescence (PL) properties and electron–phonon coupling (EPC) reflected in the multi-phonon Raman spectra. The Raman and PL spectra were studied at different powers of the exciting laser radiation (P _exc). The spectral position and width of the phonon Raman peaks and the near bandgap PL band at low P _exc are supposed to be determined by the structural quality of the surfaces/boundaries of the crystallites. The intensity of the near-bandgap and defect-related PL and the magnitude of the EPC are additionally affected by the dopant concentration. Because of the large crystallite size (>30 nm, determined from XRD), the effects of phonon or electron confinement are negligible in these nanostructures. The behaviour of the position and width of phonon and PL bands with increasing P _exc indicates that the heat dissipation in the film, which is dependent on the nanostructure morphology and Ag content, plays an important role. In addition, the cytotoxicity of ZnO:Ag nanostructures was investigated by using monolayer cell cultures of epithelioid origin Madin-Darby bovine kidney and Madin-Darby canine kidney cells at a MTT assay revealing that the level of silver doping of ZnO nanostructures, their morphology, and geometric dimensions determine their toxic effects.