Both root architecture and plant N nutrition are altered by inoculation with the plant growth-promoting rhizobacteria (PGPR) Phyllobacterium strain STM196. It is known that NO3- and N metabolites can act as regulatory signals on root development and N transporters. In this study, we investigate the possible interrelated effects on root development and N transport. We show that the inhibition of Arabidopsis lateral root growth by high external NO3- is overridden by Phyllobacterium inoculation. However, the leaf NO3- pool remained unchanged in inoculated plants. By contrast, the Gln root pool was reduced in inoculated plants. Unexpectedly, NO3- influx and the expression levels of AtNRT1.1 and AtNRT2.1 genes coding for root NO3- transporters were also decreased after 8 days of Phyllobacterium inoculation. Although the mechanisms by which PGPR exert their positive effects remain unknown, our data show that they can optimize plant development independently from N supply, thus alleviating the regulatory mechanisms that operate in axenic conditions. In addition, we found that Phyllobacterium sp. elicited a very strong induction of AtNRT2.5 and AtNRT2.6, both genes preferentially expressed in the shoots whose functions are unknown.