This study aimed to develop and evaluate hydrogels containing a cyclodextrin complex with clove essential oil and other free volatile oils with antimicrobial properties (tea tree and rosemary essential oils), focusing on their pharmaco-technical and rheological characteristics. The formulations varied in the Carbopol 940 (a hydrophilic polymer) and volatile oils’ concentrations. Rheological analysis indicated that the gels displayed pseudoplastic behavior, with the flow index (n) values below 1, ensuring appropriate consistency and handling. The results showed that increasing the Carbopol concentration significantly enhanced the yield stress, consistency index, and viscosity, with gel B, containing 1% Carbopol, 1.5% tea tree essential oil, and 1.5% rosemary essential oil, demonstrating optimal stability and rheological properties. At the same time, the concentration of volatile oils was found to modulate the gels’ flow parameters, but their effect was less pronounced than that of the gel-forming polymer. Antimicrobial testing revealed that both gel B and gel E (containing 1% Carbopol, 2% tea tree essential oil, and 2% rosemary essential oil) exhibited antimicrobial activity against Gram-positive, Gram-negative bacteria, and Candida spp., with gel E showing superior efficacy against Candida tropicalis. The antimicrobial effects were likely influenced by the higher concentrations of tea tree and rosemary essential oils in gel E. Overall, the study demonstrates that the concentration of Carbopol 940 primarily determines the gel’s rheological behavior, while volatile oil concentration modulates antimicrobial effectiveness.