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Urinary tract infections are common in small animal practice, with Escherichia coli and Klebsiella pneumoniae being the primary causative agents. Bacterial resistance to synthetic antimicrobials has driven the search for natural alternatives, such as essential oils, whose direct application is limited by their volatility and instability. The objective of this study was to characterize, both physicochemically and morphologically, alginate capsules containing a mixture of essential oils from Origanum vulgare L. and Thymus vulgaris L., as well as to evaluate, in a complementary manner, their antibacterial activity against uropathogenic bacteria isolated from dogs and cats. The capsules were obtained by ionic gelation and characterized in terms of physical properties, water activity, moisture content, and morphology. Antibacterial activity was evaluated using the agar diffusion method. The encapsulated systems exhibited parameters consistent with good flowability, physicochemical stability, and a water activity below 0.7. Furthermore, the capsules containing the essential oils maintained antibacterial activity, evidenced by the formation of inhibition zones against the evaluated strains. It is concluded that alginate encapsulation constitutes a promising strategy for the protection and application of essential oils with potential use in the control of uropathogenic pathogens in veterinary medicine.