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Bioaugmentation promises benefits for agricultural production as well as for remediation and phytomining approaches. Thus, this study investigated the effect of soil inoculation with the commercially available product RhizoVital^®42, which contains <i>Bacillus amyloliquefaciens</i> FZB42, on nutrient uptake and plant biomass production as well as on the phytoaccumulation of potentially toxic elements, germanium, and rare earth elements (REEs). <i>Zea mays</i> and <i>Fagopyrum esculentum</i> were selected as model plants, and after harvest, the element uptake was compared between plants grown on inoculated versus reference soil. The results indicate an enrichment of <i>B. amyloliquefaciens</i> in inoculated soils as well as no significant impact on the inherent bacterial community composition. For <i>F. esculentum</i>, inoculation increased the accumulation of most nutrients and As, Cu, Pb, Co, and REEs (significant for Ca, Cu, and Co with 40%, 2042%, and 383%, respectively), while it slightly decreased the uptake of Ge, Cr, and Fe. For <i>Z. mays</i>, soil inoculation decreased the accumulation of Cr, Pb, Co, Ge, and REEs (significant for Co with 57%) but showed an insignificant increased uptake of Cu, As, and nutrient elements. Summarily, the results suggest that bioaugmentation with <i>B. amyloliquefaciens</i> is safe and has the potential to enhance/reduce the phytoaccumulation of some elements and the effects of inoculation are plant specific.