Supported ionic liquid (SIL) membranes using imidazolium based ionic liquids and hydrophobic PTFE base membrane were used for the pi electron mediated separation of aromatic compounds including dyes in aqueous and non-aqueous medium. The FTIR of SIL membranes showed the signature of the functionalities for both base membrane and the imidazolium moiety. A significant reduction in contact angle, especially the dynamic contact angle, was observed for SIL membranes compared to the virgin membrane indicating the enhancement in surface hydrophilicity of the membrane, while considerable changes zeta potential was seen at different pH indicating the modification in surface charge. The SEM image confirmed the pore filling of base membrane with ionic liquids. The stability of the SIL membranes were studied using hexane, water and DMF as solvents. Tuning the anionic moieties, ionic liquids were utilized for aqueous and non-aqueous application through SIL membranes. For non-aqueous applications, the trend in separation efficiency was found to be divinylbenzene > styrene > toluene, which was attributed to the more p electron cloud density on extended conjugation leading to favorable interaction with ionic liquid influencing its transfer through SIL membranes. Preferential separation of Congo red (CR) and Ramazol Brilliant Blue R (RBBR) was achieved in water based application of the SIL membranes. The anti-microbial activity of these SIL membranes were investigated using gram-positive bacteria (Staphylococcus aureus and Pseudomonas aeruginosa). More the number of carbon atom on the side chain of the imidazolium ring, more antimicrobial activity was observed.