Novel derivatives of pyrano[2,3‐b]pyridine and pyrrolo[2,3‐b]pyrano[2.3‐d]pyridine were prepared, and their structures were elucidated by spectral and elemental analyses. The newly prepared candidates were evaluated for their antimicrobial activity against Candida sp., Aspergillus multi, Aspergillus niger, Escherichia coli, and Staphylococcus aureus. All the tested compounds revealed potent to moderate activity toward all tested microorganisms; especially, candidate 10 showed comparable antifungal activity as that showed by the standard drug ketoconazole toward Candida sp., and ethyl 4‐methyl‐1,7,8,9‐tetrahydropyrano[2,3‐b]pyrrolo[2,3‐d]pyridine‐3‐carboxylate (12) was the most active compound against all the tested bacteria. Furthermore, the newly synthesized compounds are subjected to molecular docking study for the inhibition of the enzyme L‐glutamine: D‐fructose‐6‐phosphate amidotransferase [GlcN‐6‐P], which is a new target for antimicrobials to explain action mode of these target compounds as leads for discovering other antimicrobial agents.