Abiotic stress is one of the main factors that cause a decline in plant growth and productivity. The use of microorganism-based biofertilizers can be an environmentally friendly alternative to enhance plant resistance to extreme environmental conditions. This study aims to analyze the role of microorganisms in biofertilizers on the profile of fatty acids and squalene related to plant abiotic stress resistance. Metabolite analysis was carried out using a metabolomic approach and metabolic pathway mapping through the KEGG database. Identification results showed the presence of important compounds such as palmitic acid, oleic acid, stearic acid, phytol, squalene, alpha-tocopherol, stigmasterol, and sitosterol. These compounds play a role in cell membrane stability, antioxidant activity, and protection against oxidative stress. Pathway analysis shows the involvement of the Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway, which is related to membrane metabolism and the cellular response to environmental stress. The research results indicate that microorganisms in biofertilizers have the potential to enhance plant adaptation to abiotic stress through the regulation of lipid metabolism and the production of bioactive compounds. Thus, microorganism-based biofertilizers can be developed as an environmentally friendly alternative to support sustainable agriculture.