This study investigated the effect of whole wheat flour partially replaced by sprouted whole wheat flour on phenolic profile, dough rheological properties and bread characteristics. A 3 × 3 factorial design was used to evaluate three sprouting times (24, 48 and 72 h) and three replacement percentages (5, 15 and 25%) compared to the control sample (whole wheat flour). Total amylolytic activity (+43%), α-amylase (+73%) and antioxidant activity (+3.8 times higher) of flours progressively increased with sprouting times. However, it did not change the total phenolic content. The progressive increase of sprouting time and replacement levels can negatively impact the dough and bread-making due to a weakened gluten network and reduced dough strength caused by the increased enzymatic action. Moreover, bread firmness and chewiness were significantly increased. Eighty-eight phenolic compounds were annotated by metabolomics tools. Phenolic acids had the highest ion abundance due to the isomers of ferulic acid. Principal Components Analysis showed great variability of phenolic compounds abundance in sprouting time (99%) and replaced flours (87%). These results suggest that sprouted wheat flours can be incorporated into baked products, although improving the bread characteristics is highly dependent on the sprouting time and its replacement levels.