The importance of the valorization of industrial by-products has led to increasing research into their reuse. In this research, the innovative by-product okara oat flour, derived from the vegetable beverage industry, was studied. Oat okara sourdough was also produced and evaluated. The microbiological identification and typing involved bacterial and yeast isolates from both flour and sourdough. Untargeted metabolomics allowed the identification of biomarkers of fermented flour, such as phenolic classes, post-fermentation metabolites, fatty acids, and amino acids. The microorganisms most found were Weissella confusa, Enterococcus faecium, Pediococcus pentosaceus, and Pichia kudriavzevii, while Saccharomyces cerevisiae appeared only at the end of the sourdough’s back-slopping. Untargeted metabolomics identified a total of 539 metabolites, including phenolic compounds, lipids, amino acids, and organic acids. An increase in polyphenols released from the food matrix was detected, likely because of the higher bio-accessibility of phenolic metabolites promoted by microbial fermentation. Fermentation led to an increase in isoferulic acid, p-coumaric acid, sinapic acid, and a decrease in amino acids, which can be attributed to the metabolism of lactic acid bacteria. Some key markers of the fermentation process of both lactic acid bacteria and yeast were also measured, including organic acids (lactate, succinate, and propionate derivatives) and flavor compounds (e.g., diacetyl). Two bioactive compounds, such as gamma-aminobutyric acid and 3-phenyl-lactic acid had accumulated at the end of fermentation. Taken together, our findings showed that oat okara flour can be considered an excellent raw material for formulating more sustainable and functional foods due to fermentation promoted by autochthonous microbiota.