Two new series of quinoline incorporated benzimidazole derivatives (4a-i and 8a-f) were synthesized from substituted aniline and isatin through multi-step reaction. 6-substituted-4-carboxyquinolines (3a,b and 7) were synthesized by multi component one pot reactions (via Doebner reaction and Pfitzinger reaction respectively) and the targeted benzimidazole derivatives were obtained by the reaction of 6-substituted-4-carboxyquinolines (3a,b and 7) with substituted aromatic diamines in acidic media. All the newly synthesized compounds were characterized by IR, NMR mass spectral study and also by C, H, N analyses. The final compounds were screened for their in-vitro antibacterial and antifungal activity by well plate method (zone of inhibition). The results revealed that, compounds 4c, 4d, 8c and 8d showed significant antibacterial activity. The compound 8b was found to be potent antifungal agent. 4a, 8a and 8f showed moderate to good antimicrobial activity as compared to the standard drugs against all tested microbial strains.