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Some of the challenges of yeast encapsulation protocols are low phytochemical internalization rates and limited intracellular compartments of yeasts. This study uses an ultrasound‐assisted batch encapsulation (UABE) protocol to optimize the encapsulation of curcumin and fisetin by recovering nonencapsulated biomaterial and further incorporating it into nonloaded yeasts in three encapsulation stages (1ES, 2ES and 3ES). The effect of selected acoustic energies (166·7 and 333·3 W l−1) on the encapsulation efficiency (EE), yield (EY) and antioxidant activity retention were evaluated, and then, compared with a control process (without ultrasound treatment). Compared to the control, enhanced EEs were achieved for both curcumin (10·9% control to 58·5% UABE) and fisetin (18·6% control to 76·6% UABE) after 3ES and the use of 333·3 W l−1. Similarly, the yeast maximum loading capacity was improved from 6·6 to 13·4 mg g−1 for curcumin and from 11·1 to 26·4 mg g−1 for fisetin after UABE protocol. The antioxidant activity of produced biocapsules was positively correlated with the bioactive‐loaded content of yeasts when ultrasound treatment was applied. Overall, results from this study provide valuable information regarding UABE processes, and moreover, bring new and creative perspectives for ultrasound technology in the food industry. [ABSTRACT FROM AUTHOR]