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Description: Azolla spp. are floating ferns that establish permanent symbiosis with the nitrogen-fixing bacteria Trichormus azollae and, for this reason, have been used for centuries as sustainable biofertilizers to enrich the soil with inorganic nitrogen and improve rice yield. However, the molecular interactions between Azolla and co-cultivated rice plants only recently started to be thoroughly investigated. In this study, we exploited an experiment in which rice plants were grown together with Azolla by maintaining a low and constant concentration of inorganic nitrogen. We employed a combination of non-targeted metabolomics, chemometrics, and molecular networking to dissect the impact of Azolla co-cultivation on the metabolome of rice roots- and leaves, as well as to identify the metabolites released by Azolla into the growing medium. Our analyses showed that Azolla can synthesize and release a broad range of metabolites in the culture medium, mainly comprising small peptides (i.e., di- and tri-peptides) and flavonoids, that may have stimulated the rice plant growth. Moreover, we observed a systematic response in the upregulation of rice metabolites that started from the roots and shifted, over time, to the leaves. Metabolomics analysis indicated that during the first stages of co-cultivation, the impact of Azolla on rice mainly resulted in the accumulation of small peptides, lipids and carbohydrates in roots, as well as flavonoid glycosides and carbohydrates in leaves. Consistent with these results, transcriptomics analysis of rice roots indicated significant changes in the expression of genes coding for small peptide and lipid transporters and genes involved in the pathways of amino acid salvage and biosynthesis. Overall, our study provides new insights into Azolla’s beneficial and growth-promoting effects on rice. Further understanding of the molecular mechanisms by which Azolla functions as a biostimulant in rice co-culture could facilitate the development of more sustainable and environmentally friendly techniques to increase yields.