Plant-based beverages made from protein-rich raw materials are gaining popularity due to the increasing demand for sustainable food production. However, these beverages may suffer from undesirable sensory or nutritional properties. To address these challenges, fermentation could be employed in their production. We employed lactic acid bacteria, spontaneous fermentation, and kombucha fermentation, followed by LC–MS metabolomics analysis, to investigate the changes in the biochemical composition of fermented beverages using lupin, a less-utilized protein-rich plant, as the raw material. After fermentation with individual lactic acid bacteria strains, as well as with spontaneous and kombucha fermentations involving various microbial species, we observed distinct differences among these fermentations. For instance, the relative abundances of biogenic amines and raffinose family oligosaccharides (RFOs) varied depending on the fermentation technique used. Additionally, the relative abundances of lactic acid derivatives increased in all fermentations. The results of this study demonstrate that fermentation can effectively modify the biochemical composition of lupin-based beverages. By selecting the appropriate fermentation technique, lupins could be used to produce sustainable protein-rich beverages with possibly improved nutritional content.