We report an efficient sustainable two-step anion exchange synthetic procedure for the preparation of choline API ionic liquids (Cho-API-ILs) that contain active pharmaceutical ingredients (APIs) as anions combined with choline-based cations. We have evaluated the in vitro cytotoxicity for the synthesized compounds using three different cells lines, namely, HEK293 (normal kidney cell line), SW480, and HCT 116 (colon carcinoma cells). The solubility of APIs and Cho-API-ILs was evaluated in water/buffer solutions and was found higher for Cho-API-ILs. Further, we have investigated the antimicrobial potential of the pure APIs, ILs, and Cho-API-ILs against clinically relevant microorganisms, and the results demonstrated the promise of Cho-API-ILs as potent antimicrobial agents to treat bacterial infections. Moreover, the aggregation and adsorption properties of the Cho-API-ILs were observed by using a surface tension technique. The aggregation behavior of these Cho-API-ILs was further supported by conductivity and pyrene probe fluorescence. The thermodynamics of aggregation for Cho-API-ILs has been assessed from the temperature dependence of surface tension. The micellar size and their stability have been studied by dynamic light scattering, transmission electron microscopy, and zeta potential. Therefore, the duality in the nature of Cho-API-ILs has been explored with the upgradation of their physical, chemical, and biopharmaceutical properties, which enhance the opportunities for advances in pharmaceutical sciences.