Imidazolium-based ionic liquids (ILs) containing cleavable carbonate linkages, 1-alkyloxycarbonyloxyethyl-3-methylimidazolium chlorides with alkyl chains of 10, 12, and 14 carbon atoms, were synthesized, and their self-assembly behavior and antimicrobial activity were investigated. Differential scanning calorimetry and polarized optical microscopy studies reveal that carbonate-functionalized ILs form stable thermotropic smectic liquid-crystalline phases over a wide range of temperature. The surface activity and aggregation behavior of these new ILs were investigated by tensiometry, conductometry, potentiometry, and spectrofluorimetry. The size of aggregates was examined by dynamic light scattering (DLS). Carbonate-functionalized ILs display a higher adsorption efficiency and a lower critical micelle concentration (cmc) than simple alkyl-chain-substituted ILs. The insertion of a carbonate ester moiety in the alkyl side chain favors adsorption at the airwater interface and micellization in the bulk solution when compared to nonfunctionalized ILs. DLS measurements show that small micellelike aggregates are spontaneously formed above the cmc. Furthermore, carbonate-functionalized ILs were examined for their antimicrobial activity against a panel of clinically relevant microorganisms. Biological activity was found to increase with hydrophobicity. The presence of a carbonate ester moiety significantly enhances the antimicrobial efficiency as compared to nonfunctionalized ILs, with the susceptibility of Staphylococcus sp. toward the action of these compounds being particularly remarkable. It has been demonstrated that the functionalization of the alkyl side chain of the imidazolium salts can not only modify the aggregation behavior but also lead to differences in both efficiency and the spectrum of antimicrobial activity of amphiphilic ILs.