The present study aims to valorize the apple peels (AP) and grape seeds (GS) by the fortification of the yogurts using their powder. Firstly, the optimization of the extraction parameters for assessing maximum of total phenolic content (TPC) was achieved. Under the optimized conditions, the experimental maximum yields of TPC were 19.33 ± 2.33 and 240.59 ± 4.77 mg Gallic Acid Equivalents (GAE)/100 g Dry Weight (DW) for AP and GS, respectively, which was in close agreement with predicted values (19.32 ± 0.91 and 242.26 ± 11.08 mg GAE/100 g DW for AP and GS, respectively). The antioxidant capacity of GS extract was better with IC50 of 12.22 ± 0.89 and 225.47 ± 7.10 µg/ml in DPPH and phosphomolybdenum assays, respectively. Besides, powder from these by‐products was incorporated into yogurt samples. The classification test revealed that the yogurt prepared with GS powder was the preferred one. Practical applications Natural products rich in antioxidants are increasingly in demand for their use to preserve, in particular, the perishable foods such as dairy products. Apple and grape are widely consumed fruits and they generate an enormous amount of waste, including peels and seeds. These by‐products are valuable sources of natural antioxidants especially the phenolic compounds. In this line, the present study aims to optimize the extraction conditions to obtain the highest PC from these by‐products. Additionally, a yogurt enriched with AP and GS as natural ingredients with antioxidant virtue was produced.