Plant growth-promoting rhizobacteria (PGPR) can release volatile organic compounds (VOCs) to promote plant growth and trigger induced systemic resistance (ISR) in plants. Importantly, the release of VOCs by some PGPR strains confers improved plant uptake of nutrient elements from the soils. However, the underlying mechanisms of VOCs-regulated nutrient acquisition remained elusive. In this study, VOCs were extracted and identified from Bacillus amyloliquefaciens (strain BF06) using gas chromatographyâ€“mass spectrometry (GC-MS). BF06 VOCs exposure significantly promoted the growth and photosynthesis of Arabidopsis plants. To explore how microbial VOCs stimulate growth in plants, gene expression profiles of Arabidopsis seedlings exposed to BF06 VOCs were examined using transcriptomic analyses. In screening differentially expressed genes (DEGs), most of up-regulated DEGs related to amino acid transport, iron (Fe) uptake and homeostasis, and sulfate transport. Furthermore, BF06 VOCs significantly enhanced Fe absorption in plants under Fe limited conditions. However, when the nitric oxide (NO) synthesis was inhibited, BF06 VOCs exposure could not substantially augment Fe acquisition in plants under alkaline stress, indicating that VOCs-mediated plant uptake of Fe was required for induction of root NO accumulation. In addition, BF06 VOCs exposure led to a marked increase of some genes encoding sulfate transporters, and further increased Se accumulation in plants. Intriguingly, BF06 VOCs exposure failed to increase Se uptake in sultr1;2 mutants, which may indicate that high-level transcription of these sulfate transporters induced by BF06 VOCs was essential for enhancing Se absorption by plants. Taken together, our results demonstrated the potential of VOCs released by this strain BF06 to increase Fe and Se uptake in plants.