The necessity for the development of new antimicrobial agents due to the ever increasing threat from microbes is causing a rapid surge in research. In the present work, we have shown the efficient antimicrobial activity of a series of amino acid-based hydrogelating amphiphiles through alteration in their counterion. The subtle variation in the counterion from chloride to various organic carboxylates had a significant impact on the antimicrobial properties with notable improvement in biocompatibility toward mammalian cells. Incorporation of a hydrophobic moiety in the counterion augmented the antibacterial property of the amphiphilic hydrogelator as minimum inhibitory concentration (MIC) against the Gram-positive bacterial strain, Bacillus subtilis decreased up to 5-fold (with respect to the chloride) in the case of n-hexanoate. These counterion-varied amphiphilic hydrogelators were also found to be effective against fungal strains (Candida albicans and Saccharomyces cerevisiae) where they exhibited MICs in the range of 1.0-12.5 mu g/mL. To widen the spectrum of antibacterial activity, particularly against Gram-negative bacteria, silver nanopartides (AgNPs) were synthesized in situ within the supramolecular assemblies of the carboxylate hydrogelators. These AgNP-amphiphile soft-nanocomposites showed bactericidal property against both Gram-positive and Gram-negative bacteria. Encouragingly, these carboxylate hydrogelators showed superior biocompatibility toward mammalian cells, HepG2 and NIH3T3, as compared to the chloride analogue at a concentration range of 10-200 mu g/mL. Importantly, the AgNP composites also showed sufficient viability to mammalian cells. Because of the intrinsic hydrogelation ability of these counterion-varied amphiphiles, the resulting soft materials and the nanocomposites could find applications in biomedicine and tissue engineering.