A rational approach was adopted for the synthesis of novel series of 1-(2-(1H-benzo[d]imidazol-2-yl)-2-methyl-5-aryl-1,3,4-oxadiazol-3(2H)-yl)-3-(4-chlorophenyl)prop-2-en-1-ones 5a–n under microwave irradiation technique. Synthesized compounds were tested for their in vitro antimicrobial activity against Gram-positive, Gram-negative strains of bacteria as well as fungal strains, and in vitro cytotoxicity study (HeLa cell lines) using MTT colorimetric assay. Among the screened compounds, 5b, 5c, 5d, 5g, and 5h showed most potent antibacterial activity, while compounds 5c, 5d, 5g, and 5h emerged as the most effective antifungal agents. The structure activity relationships revealed that presence of inductively electron withdrawing groups remarkably enhances the antimicrobial activity of newly synthesized compounds. Further, the results of preliminary MTT cytotoxicity studies on HeLa cells suggested that potent antimicrobial activity of 5b, 5c, 5d, 5g, and 5h is accompanied by low cytotoxicity.