The effect of two antifungals (boscalid+kresoxim-methyl and metrafenone) applied onto vines under Good Agricultural Practices (GAPs) on the volatile composition of Tempranillo and Graciano red wines was studied. Changes in aroma profile in the wines were assessed from the combined odour activity values (OAVs) for the volatile compounds in each of seven different odorant series (viz., ripe fruits, fresh fruits, lactic, floral, vinous, spicy and herbaceous). Graciano wines obtained from grapes treated with the antifungals exhibited markedly increased concentrations of varietal volatile compounds (monoterpenes and C13-norisoprenoids) and aldehydes, and decreased concentrations of acetates and aromatic alcohols. By contrast, the concentrations of volatile compounds in Tempranillo wines showed different changes depending on the fungicide applied. Also, the aroma profiles of wines obtained from treated grapes were modified, particularly the ripe fruit nuances in Graciano wines. The OAV of this odorant series underwent an increase by more than 60% with respect to the control wine as a result of the increase of β-damascenone concentration (which imparts wine a dry plum note). The aroma profile of Tempranillo red wines containing metrafenone residues exhibited marked changes relative to those from untreated grapes.