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This study aimed to improve the effectiveness of <i>Thymus capitatus</i> and <i>Thymus algeriensis</i> essential oils (EOs), as food preservatives, through their encapsulation in different delivery systems (DSs), namely nanoemulsions and biopolymeric nanoparticles. DSs’ preparation is tailored to enhance not only physical stability but also resulting Eos’ antioxidant and antibacterial activities through different fabrication methods (high-pressure homogenization emulsification or antisolvent precipitation) and using different emulsifiers and stabilizers. DSs are characterized in terms of droplet size distribution, ζ-potential, and stability over time, as well as antioxidant and antibacterial activities of encapsulated EOs. The antioxidant activity was studied by the FRAP assay; the antibacterial activity was evaluated by the well diffusion method. EOs of different compositions were tested, namely two EOs extracted from <i>Thymus capitatus,</i> harvested from Tunisia during different periods of the year (TC1 and TC2), and one EO extracted from <i>Thymus algeriensis</i> (TA). The composition of TC1 was significantly richer in carvacrol than TC2 and TA. The most stable formulation was the zein-based nanoparticles prepared with TC1 and stabilized with maltodextrins, which exhibit droplet size, polydispersity index, ζ-potential, and encapsulation efficiency of 74.7 nm, 0.14, 38.7 mV, and 99.66%, respectively. This formulation led also to an improvement in the resulting antioxidant (60.69 µg/mg vs. 57.67 µg/mg for non-encapsulated TC1) and antibacterial (inhibition diameters varying between 12 and 33 mm vs. a range between 12 and 28 mm for non-encapsulated TC1) activities of EO. This formulation offers a promising option for the effective use of natural antibacterial bioactive molecules in the food industry against pathogenic and spoilage bacteria.