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The pathogenicity and antimicrobial properties of engineered nanomaterials (ENMs) are relatively well studied. However, less is known regarding the interactions of ENMs and agriculturally beneficial microorganisms that affect food security. Nanoceria (CeO₂nanoparticles (NPs)), multiwall carbon nanotubes (MWCNTs), graphene nanoplatelets (GNPs), and carbon black (CB) have been previously shown to inhibit symbiotic N₂fixation in soybeans, but direct rhizobial susceptibility is uncertain. Here,Bradyrhizobium diazoefficiensassociated with symbiotic N₂fixation in soybeans is assessed, evaluating the role of soybean root exudates (RE) on ENM–bacterial interactions and the effects of CeO₂NPs, MWCNTs, GNPs, and CB on bacterial growth and gene expression. Although bacterial growth is inhibited by 50 mg L⁻¹CeO₂NPs, MWCNTs, and CB, all ENMs at 0.1 and 10 mg L⁻¹cause a global transcriptomic response that is mitigated by RE. ENMs may interfere with plant‐bacterial signaling, as evidenced by suppressed upregulation of genes induced by RE, and downregulation of genes encoding transport RNA, which facilitates nodulation signaling. MWCNTs and CeO₂NPs inhibit the expression of genes conferringB. diazoefficiensnodulation competitiveness. Surprisingly, the transcriptomic effects onB. diazoefficiensare similar for these two ENMs, indicating that physical, not chemical, ENM properties explain the observed effects.