The nanoparticles (NPs) formed byEnterococcus thailandicus, Pseudomonas putida, Marinobacter hydrocarbonoclasticus, andP. geniculatewere tested against soft rot/blackleg genera. The effects of NPs recorded on bacterial DNA, proteins, and carbohydrates concentration ofPectobacterium carotovorum subsp. carotovorum, Enterobacter cloacae(soft rot), andDickeya solani(soft rot/blackleg). Treated cells showed degradation in isolated DNA, decreased proteins and carbohydrates concentration compared with untreated cells. Using Scanning Electron Microscope (SEM), the treated cells showed collapsed and small pits in the cell wall. Using Transmission Electron Microscope (TEM), internal changes showed penetration of NPs inside the tested bacterial cells, the appearance of periplasmic space, formation of vacuoles, and condensation of cytoplasm. Disease severityex vivoof potato tuber infected with tested genera demonstrated that NPs treatment didn’t show any rotted tissue compared with untreated. The ability to uptake and accumulate FeNPs from the soil in potato (Solanum tuberosum) seedlings; Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES) was used. It recorded an increase in iron content of treated potato (Solanum tuberosum) seedlings with NPs, compared with untreated. FeNPs can be used to control soft rot/blackleg diseases, instead of copper pesticides. It could be a new, approach for disease management and increase the plant’s nutritional value.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12934-023-02101-6.