Saudi Arabia has several fragrant, decorative, and medicinal plants with strong bioactivity. The current work examines the metabolite profiling of Fenugreek (Trigonella foenum-gracum L) ethanol extract for antibacterial, antifungal, antioxidant, and anticancer properties. Additionally, a computer-supported study will determine the pharmacokinetic characteristics and toxicity of the recognized mixes. The moisture, fiber, ash, protein, fat, and carbs in fenugreek seed were 4%, 6.50%, 3.20%, 28.55%, 4%, and 62.48%, respectively. Fenugreek seed flour had physiochemical properties like other edible oils. Aspergillus flavus, Escherichia coli, Staphylococcus aureus, and Salmonella typhimurium were examined for fenugreek seed flour inhibitory activity. Seed oil was found to be highly antibacterial against all tested microbes. Antimicrobial activity was strongest against E. coli, with a 20-mm inhibition zone. The highest antibacterial activity was 100% inhibition against Aspergillus flavus. The computational modeling reveals that fenugreek compounds bind the TyrRS from S. aureus, the human peroxiredoxin 5, and aspartic proteinase from C. albicans with high binding scores that reach − 9.4 kcal/mol and established promising molecular interactions with some key residues, that satisfactorily explain the in vitro results. According to the study, fenugreek seed is an important antibacterial and antifungal agent for food preservatives and medicine.