The application of ozonated water in the vineyard is an increasingly popular tool for disease management, but the quality of grapes and resulting wines is likely to be affected. Endotherapy, or trunk injection, is a particularly useful method to apply phytosanitary products since many fungal pathogens colonize the grapevine woody tissues. Thus, the present study aimed to evaluate the effect on wine quality of the ozonated water applied to Bobal grapevines, one of the most cultivated red varieties in Spain, through endotherapy (E) or its combination with spraying (E + S). Endotherapy was carried out four times before harvest for both E and E + S treatments, and spraying was performed 2 days before and after each endotherapy application. Grapes were harvested, vinified, and the quality of the finished wines was evaluated through several enological parameters and the phenolic and volatile composition. Both treatments resulted in less alcoholic and more acidic wines. The E treatment, although it reduced the content of phenolic acids, stilbenes and flavanols, significantly increased anthocyanins, whereas E + S decreased the overall amount of phenolics, which had different implications for wine colour. In terms of aroma, both treatments, but E to a greater extent, reduced the content of glycosylated precursors and differentially affected free volatiles, both varietal and fermentative. Thus, the dose of ozonated water, frequency and/or method of application are determining factors in the effect of these treatments on wine quality and must be carefully considered by winegrowers to establish the optimum treatment conditions so as not to impair the quality of wines.