To understand the impact of environmental deposition of CuO and ZnO nanoparticles (NPs) on the production of bacterial metabolites, we examined the effects of their sub-lethal levels on the production of a pyoverdine (PVD) siderophore in a plant-beneficial bacterium, Pseudomonas chlororaphis O6 (PcO6). The NPs were characterized for size, shape, surface charge and ion release. Production of PVD by the cells was evaluated by fluorimetry and the expression of genes for PVD biosynthesis and export. The level of PVD in the presence of ZnO NPs was similar to that with Zn ions at 24 h, but the NPs maintained higher level than control at 48 h. In contrast, the reduction in PVD by CuO NPs was not duplicated by Cu ions. Expression of a gene encoding an inner membrane PVD transporter was inhibited by CuO NPs, supporting the observed low amounts of external PVD detected in those cells. These findings revealed NP-specific effect for CuO NPs on PcO6 metabolism, while for ZnO NPs, the release of ions was important. Because siderophores are part of the chemical communication between soil microbes and plants, the outcomes of plant-microbe interactions could be affected by responses to NPs.