Two series of long chain imidazolium- and pyridinium-based ionic liquids containing an ester functional group in the alkyl side chain, 3-methyl-1-alkyloxycarbonylmethylimidazolium bromides (C(n)EMeImBr) and 1-alkyloxycarbonylmethylpyridinium bromides (C(n)EPyrBr), were synthesized and their thermal stability, aggregation behavior in aqueous medium, and antimicrobial activity investigated. The introduction of an ester group decreased the thermal stability of the functionalized ILs compared to simple alkyl chain containing ILs (1-alkyl-3-methylimidazolium bromides and 1-alkylpyridinium bromides). Tensiometry, conductimetry, and spectrofluorimetry were applied to study the self-aggregation of the amphiphilic ILs in aqueous solution. The ILs investigated displayed surface activity and the characteristic chain length dependence of the micellization process of surfactants. As compared to simple alkyl chain containing ILs bearing the same hydrocarbon chain, ester-functionalized ILs possess higher adsorption efficiency (pC(20)) and significantly lower critical micelle concentration (cmc) and surface tension at the cmc (γ(cmc)), indicating that the incorporation of an ester group promotes adsorption at the air/water interface and micelle formation. The antimicrobial activity was evaluated against Gram-negative and Gram-positive bacteria and fungi. ILs containing more than eight carbon atoms in the alkyl chain showed antimicrobial activity. Their efficiency as antimicrobial agents increased with the hydrophobicity of the amphiphilic cation being the C(12) homologous the most active compounds. The incorporation of an ester group particularly increased the biological activity against fungi.