Adlay millet seeds are well known for excellent health benefits. However, using fungal fermentation to improve their nutritional and functional constituents and the underlying mechanisms has not been thoroughly investigated. Herein, we used
Rhizopus oryzae
as starter and applied metabolomics combining with quantitative verification to understand the changes of the nutritional and functional profiles of adlay millet seeds. Results showed that a total of 718 metabolites from 18 compound classes were identified. The fermentation with
R. oryzae
varied 203 differential metabolites, of which 184 became more abundant and 19 got less abundant, and many components such as amino acids, nucleotides, vitamins, flavonoids, terpenoids, and phenols significantly increased after the fermentation process. Interestingly, we found that
R. oryzae
synthesized high levels of two important beneficial compounds, S-adenosylmethionine (SAMe) and β-Nicotinamide mononucleotide (β-NMN), with their contents increased from 0.56 to 370.26 μg/g and 0.55 to 8.32 μg/g, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of enriched metabolites revealed the amino acid metabolic pathways were important for conversion of the primary and secondary metabolites. Specifically, aspartate can up-regulate the biosynthesis of SAMe and β-NMN. These findings improved our understanding into the effects of
R. oryzae
fermentation on enhancing the nutritional and functional values of cereal foods.