In the field of interphase and colloidal science, the interest in the research of ionic liquid (IL) has been growing specifically when surface active ionic liquids (SAILs) emerged in this field. Herein, we report the synthesis of Halogen-free COOH-functionalized Imidazolium and Pyridinium-based SAILs. The surface activity and aggregation behavior of synthesized SAILs were investigated using the electric conductivity, surface tension, fluorescence quenching, density, and speed of sound. In addition, the thermodynamic parameters and the critical micellar concentration dependency on temperature were also investigated using charged pseudo-phase model. The micellization process was found spontaneous and entropy-driven in the temperature range of 25°–45 °C of synthesized SAILs. Furthermore, the average aggregation number was determined by the speed of sound, fluorescence quenching, and density. In addition, the antimicrobial activity of the synthesized SAILs was studied, which shows a broad spectrum of antimicrobial activity against Gram-positive and Gram-negative bacteria. The introduction of an acid group enhanced the antimicrobial activity significantly as compared to non-functionalized ILs.