A set of methylimidazolium-furanchalcone hybrids and 1-alkyl-3-methylimidazolium salts were tested in order to find their antimicrobial activity against five gram positive bacteria, two gram negative bacteria and three fungi. In the series of 1-alkyl-3-methylimidazolium salts, compounds 4 and 7 were the most active compounds against S. mutans and F. oxysporum, respectively (MIC value of 3.0 and 6.7 mM, respectively). In addition, among the hybrid molecules, compound 10 exhibited the highest activity against F. solani (MIC50 = 14.3 mM) followed by hybrid 11 (MIC50 = 14.5 mM), which was also the most active against S. aureus, S. mutans (MIC50 = 14.6, 18.7 mM, respectively). The activity of these hybrids was even better with regard to the lead compounds (furanchalcone, methylimidazole or the mixture). In the structure-activity relationship there was observed higher bioactivity when the alkyl linker had eigth carbon atoms. This was then supported by the in silico study which displayed a strong relationship between the length of the alkyl chain on N and the biological activity. The results highlight the importance of these derivatives (1-alkyl-3-methylimidazolium salts) and hybrids (methylimidazolium-furanchalcone) as potential antimicrobial agents.