In Peru, wheat (Triticum aestivumL.) is one of the main resources in the food industry; however, due to its low harvested area, it is the second most imported cereal. The quality of wheat flour was studied to verify that it has desirable characteristics for the preparation of bakery products. The quality of commercial and monovarietal wheat flours was assessed by measuring their physicochemical and rheological parameters, as well as the gluten content and wheat protein fractions. Eight commercial wheat flours and four monovarietal wheat flours (Barba negra, Candeal, Espelta, and Duro) from Peru were evaluated. Commercial wheat flours presented significantly higher levels of protein and gluten index compared to monovarietal wheat flours (p< 0.05). Between both groups, no significant differences were observed in the content of wet and dry gluten. Interestingly, monovarietal wheat flours presented a higher percentage of gliadins and albumins/globulins, as well as lower levels of glutenin, compared to commercial wheat flours (p< 0.05). According to the logistic regression models, the baking strength (W) was the most important parameter to evaluate the quality of commercial and monovarietal wheat flours. Our results show that monovarietal wheat flours show a lower quality compared to commercial wheat flours.