Pumpkin seeds are by‐products that are discarded as household and agricultural waste or used as animal feed. Pumpkin seeds have many nutritional properties, especially antioxidant activity. Therefore, they have the potential to be used as foods with appropriate bioactive characteristics. Encapsulation is an effective method for protecting bioactive compounds. To strengthen the alginate hydrogel network, chitosan coating was used. After that, different concentrations (50, 100, and 150 mg per 100 ml drink) of free and microcapsulated pumpkin seed protein hydrolysate (PSPH) were added to aloe drink to investigate its antioxidant activity and its physicochemical properties during storage at refrigerator temperature (30 days at 4°C). According to the results, pancreatin hydrolysates showed higher antioxidant activities (52.6% DPPH, 91.1% iron chelation activity, and 1.0 (absorbance at 695 nm) total antioxidant activity), so this sample was chosen as the core material for encapsulation. The encapsulation efficiency of plain alginate and chitosan‐alginate beads was 71.63 ± 2.15% and 81.4 ± 2.8%, respectively. The results of the drink analysis showed that by adding PSPH, bitterness rose. On the other hand, by increasing the concentration of beads, acidity decreased (0.15 ± 0.02%); also, pH (4.45 ± 0.05), dissolved particles (19.7 ± 0.83), ash (0.34 ± 0.05%), color intensity (0.62 ± 0.15), and antioxidant activity (50.4 ± 1.5% and 47.5 ± 1.3%, respectively, in DPPH and Fe chelation activity) increased. However, with the increase in free protein hydrolysate concentration, acidity (0.34 ± 0.05%), dissolved particles (19.8 ± 0.87), ash (0.36 ± 0.05%), color intensity (0.88 ± 0.2), and antioxidant activity (56.5 ± 1.8% and 50.1 ± 1.5%, respectively, in DPPH and Fe chelation activity) increased but pH (3.45 ± 0.04) decreased. Additionally, it should be noted that the decrease in antioxidant activity and pH and increase in acidity in the samples containing protein hydrolysate occurred at a higher speed than the samples containing beads. By adding chitosan‐alginate microcapsules to drinks, all microbial tests were negative, and PSPH in higher concentrations could inhibit microbial growth. Above all, the results showed the positive effect of adding multilayer hydrogels on increasing shelf life and improving the taste and antioxidant properties of aloe vera drinks.