Knowledge of the structure–activity relationship (SAR) allows for the possibility to design and synthesize new cationic amphiphiles with optimized antimicrobial activities for future development of new disinfectants, sanitizers or preservatives. The need to design and identify new compounds, possessing antimicrobial properties, results from the emergence of more resistant micro-organisms in our globalized society. Hitherto, most studies which analyse the biological activity of ionic liquids (ILs) investigate the effect of the cation, whereas the knowledge of the effect of the anion is limited. The present study confirms the existence of a strong relationship among structure, surface activity and biological action of imidazolium ionic liquids on bacteria and fungi. The dependence of the antimicrobial activity on chemical structure–chain length and anion type of 30 compounds was determined. The anion is an important structural element which partakes in the definition of the phyiscochemical properties of the IL, and in consequence the technological applications and mode of action of the compound. The introduction of a longer substituent on the imidazolium cation results in a lower minimal inhibitory concentration (MIC). Thus, antifungal and antibacterial activities were found to increase with chain length, very often up to a point exhibiting a cut-off effect at chain lengths of 16 or 18 for the imidazolium cation and the [Cl] anion. The efficiency of surface tension reduction circumscribed by the pC₂₀ and the relationship between antimicrobial activity and pC₂₀ is described herein. The relationship indicates an antimicrobial mode of action dependant on the surface activity of the molecule, inferring that surface activity may contribute to the cut-off effect in the biological activity of ILs.