Brazilian ethanol fermentation process commonly uses baker's yeast as inoculum. In recent years, wild type yeast strains have been widely adopted. The two more successful examples are PE-2 and CAT-1, currently employed in Brazilian distilleries. In the present study, we analyzed how these strains compete for nutrients in the same environment and compared the potential characteristics which affect their performance by applying quantitative proteomics methods. Through the use of isobaric tagging, it was possible to compare protein abundances between both strains during the fermentation process. Our results revealed a better fermentation performance and robustness of CAT-1 strain. The proteomic results demonstrated many possible features that may be linked to the improved fermentation traits of the CAT-1. Proteins involved in response to oxidative stress (Sod1 and Trx1) and trehalose synthesis (Tps3) were more abundant in CAT-1 than in PE-2 after a fermentation batch. Tolerance to oxidative stress and trehalose accumulation were subsequently demonstrated to be enhanced for CAT-1, corroborating the comparative proteomic results. The importance of trehalose and the antioxidant system was confirmed by using mutant stains deleted in Sod1, Trx1 or Tps3. These deletions impaired fermentation performance, strengthening the idea that the abilities of accumulating high levels of trehalose and coping with oxidative stress are crucial for improving fermentation.