Biochemical and transcriptional approaches can provide crucial evidence about the physiological changes which can occur in organic and conventional cultivated common orange [Citrus sinensis (L.) Osbeck]. This study aimed to investigate the change in physicochemical parameters, the concentrations of free amino acids and other N-containing compounds, and the expressions of key genes coding for enzymes linked to N assimilation in fruits of common orange cv. "Valencia Late". Two enzymes involved in different ways in N assimilation were considered: nitrate reductase (NR), catalyzing the conversion of nitrate into nitrite, and glutamate dehydrogenase (GDH), operating in the assimilation of ammonium (interacting with glutamate synthase), and in ammonium re-assimilation through glutamate deamination.Results showed that the different fertilizers did not affect the physicochemical characteristics of fruits but induced the different accumulation of free amino acids, with higher concentrations of proline and contemporarily lower concentrations of glutamate, in addition to upregulated the expression of GDH gene in fruits from organically managed tress. This study identified a possible adaptive response of common orange plants to organic or conventional fertilizers. The present work is intended as a first step to make the mechanisms underlying plant responses to N supply clearer by comparing organic and conventional cultivation. It also can support breeders to select the best citrus cultivars and agronomists to improve crop fertilization and production management.