Root-associated microbiomes can influence plant nutrient acquisition and adaptation to nutrient limitation, but how nitrogen availability shapes bacterial communities in different root compartments remains incompletely understood. We used 16S rRNA gene amplicon sequencing to characterize root-zone (RE) soil and root endosphere bacterial communities in four maize inbred lines previously classified as having contrasting responses to low-nitrogen (NL) conditions grown under low- and normal-nitrogen (NZ) conditions. Nitrogen supply was significantly associated with bacterial community composition in both the RE soil (R2 = 0.09, p = 0.001) and root endosphere (R2 = 0.06, p = 0.011) whereas genotype was significantly associated with community composition in both the RE soil (R2 = 0.15, p = 0.011) and root endosphere (R2 = 0.18, p = 0.002). The nitrogen × genotype interaction was significant in the RE soil (R2 = 0.18, p = 0.003) but not in the root endosphere (R2 = 0.14, p = 0.127). Nitrogen supply significantly affected Shannon diversity in the RE soil (F = 6.20, p = 0.024), whereas its effect on root endosphere Shannon diversity was not significant after exclusion of organelle-associated ASVs (F = 0.266, p = 0.613). NL conditions enriched several genera with reported plant growth-promoting and stress-related functions, including Bacillus, Exiguobacterium, Acinetobacter, Kosakonia, and members of the Burkholderia-Caballeronia-Paraburkholderia complex. By contrast, several actinobacterial taxa were preferentially enriched under NZ conditions. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) predicted differences in pathways related to nitrogen and carbon metabolism and environmental signal transduction. Conclusions: These findings indicate that nitrogen supply and host genotype are associated with variation in maize root-associated bacterial communities in a compartment-dependent manner, with nitrogen-associated changes more evident at the level of community composition than Shannon diversity. The low-nitrogen-associated taxa identified here provide candidates for future functional evaluation.