In leguminous plants, symbiotic nitrogen (N) fixation performances and N environmental conditions are linked because nodule initiation, development and functioning are greatly influenced by the amount of available N sources. We demonstrate here that N supply also controls, beforehand, the competence of leguminous plants to perform the nodulation program. Lotus japonicus plants preincubated for 10 d in high-N conditions, and then transferred to low N before the Mesorhizobium loti inoculation, had reduced nodulation. This phenotype was maintained for at least 6 d and a complete reacquisition of the symbiotic competence was observed only after 9 d. The time-course analysis of the change of the symbiotic phenotype was analysed by transcriptomics. The differentially expressed genes identified are mostly involved in metabolic pathways. However, the transcriptional response also includes genes belonging to other functional categories such as signalling, stress response and transcriptional regulation. Some of these genes show a molecular identity and a regulation profile, that suggest a role as possible molecular links between the N-dependent plant response and the nodule organogenesis program.