Fenugreek (Trigonella foenum-graecum) is an annual dicotyledonous plant belonging to the Fabaceae family. Germination of fenugreek seeds improves its nutritional profile, and it is traditionally consumed worldwide to regulate blood glucose levels, manage the menstrual cycle, and reduce body heat. However, the metabolite differences between germinated and ungerminated seeds remain underexplored. The primary objective of this study is to profile bioactive metabolites that are differentially expressed in raw fenugreek seeds, soaked seeds (12 h), and germinated seeds. Seeds were soaked for 12 h, consistent with traditional methods used in Indian households to sprout fenugreek for consumption. After soaking, seeds were germinated for 24 and 36 h, and freeze dried. The seeds were then ground into powder, and metabolites were extracted using hexane, dichloromethane, and methanol for gas chromatography-mass spectrometry (GC–MS) analysis. Proteins were also extracted from the seeds and analyzed by LC–MS/MS-based peptide mass fingerprinting following trypsin digestion. GC–MS analysis revealed several bioactive metabolites present in germinated seeds compared to ungerminated seeds. Molecular docking studies for selected compounds were performed against targets such as Human Aldose Reductase (ALR2), Cyclooxygenase-2 (COX-2), Cytochrome P450, Protein Kinase B, and the epidermal growth factor receptor to evaluate their antidiabetic, anti-inflammatory, antibacterial, anticancer, and antioxidant activities. The differentially expressed proteins were also profiled, revealing involvement in biological functions such as ion channel movement, translation, regulation of cell cycle progression, and signal transduction pathways. These proteins were found to be glycosylated, phosphorylated, and, in some cases, acetylated. These findings suggest that germinated fenugreek seeds are rich in nutraceutical compounds. Further research to identify peptides with potent biological activity could have significant implications for the nutraceutical industry.