This study elucidates the impact of element dose during nanoparticle (NPs) synthesis on plant growth indices. Novel NPs containing two essential micro-nutrients, zinc (Zn) and manganese (Mn), were co-doped on cerium oxide (CeO2) (ZnMnCe) with different ratios (1, 2, and 3%). The synthesized NPs were characterized by advanced analytical techniques (EDX, TEM, SEM, XPS, and XRD) and hydroponically applied to barley (Hordeum vulgare L.). The impact of ZnMnCe NPs on growth indices and plant nutrients was examined. SEM, HRTEM, and confocal microscopy were used to show the morphological and structural influences of ZnMnCe NPs. Results showed that the plant growth indices (root/leaf length, chlorophyll fluorescence, pigmentation, and biomass) were remarkably improved with a 1% Mn/Zn addition. Conversely, growth retardation, cell membrane damage, root morphology deformation, and genotoxicity were apparent by 3% of Mn/Zn addition. Overall, a significant improvement in growth was revealed when Mn and Zn were included at 1%. However, increasing concentrations (2% and 3%) impaired the growth. These results show that the element ratio used in NPs synthesis is essential in the plant's physiological response. Precise adjustment of element dosage during NPs synthesis determines whether the NPs are beneficial or harmful. This must be well-balanced for nanofertilizer production and plant applications.