This study aimed to evaluate the effect of strobilurin (pyraclostrobin) + triazole (epoxiconazole) fungicides application on the proximate composition of soybeans. Six treatments of varying numbers of fungicide applications following soybean germination, termed T1 (control), T2, T3, T4, T5, and T6, were assessed for this experiment. Based on the results, there were only minor differences in the proximate composition of soybeans in terms of moisture, ash, crude protein, and total lipid contents. In contrast, there were large effects on the contents of phenolic compounds and the levels of phytosterols and tocopherols, which varied greatly among the fungicide application treatments. Multivariate statistical analysis was applied to identify critical issues regarding the potential for the production of soybeans enriched in phenolic compounds, tocopherols, and essential fatty acids (α-linolenic and linoleic acids, representatives of the omega-3 and omega-6 families, respectively) associated with the number of sprayings applied during the development of soybean crops.