In this study, glycyrrhizic acid (GA) (extracted from licorice root) and Thymus daenensis essential oils (Td-EO) were loaded into ß-cyclodextrin (ß-CD) and subsequently, were co-encapsulated with alginate to produce active alginate hydrogel beads. The structural properties, antioxidant activity, and antimicrobial features of alginate hydrogel beads incorporated with GA and Td-EO active ingredients were evaluated. The structural properties of hydrogels were analyzed using FTIR, DSC, SEM, and DLS techniques. FTIR analysis indicated no significant interaction between GA/Td-EO active agents and functional groups of alginate, resulting in an easy release of Td-EO and GA from the hydrogels. A maximum swelling capacity of ∼610.3% was obtained for alginate beads at ambient temperature. The encapsulation efficiency and loading capacity of GA/Td-EO for the hydrogel beads were in a range of between 89.12–94.06, and 1.04–3.12, respectively. Incorporation of GA and Td-EO in hydrogel beads improved antioxidant activity. Investigating the in vitro antibacterial activity of alginate beads against S. aureus (Gram-positive), and E. coli (Gram-negative) showed a high inhibition zone (21.00 ± 1.38 mm) for S. aureus. The release of Td-EO and GA from alginate beads in the simulated gastric fluid (SGF) (pH 1.2) and simulated intestinal fluids (SIF) (pH 7.4) at 37 °C were studied. In the SIF medium, a high rate release of both Td-EO and GA was observed. Release of Td-EO and GA from alginate beads can be considered as a promising candidate in designing intelligent drug carrier with intestinal release activity.