A solvent free microwave hydrodiffusion and gravity extraction (MHG) of flavonol content from onion (Allium cepa L.) was studied. Effectiveness of this innovative method in extraction of onion total phenolic content, total quercetin (TQ), quercetin aglycon (QA), quercetin-3,4′-diglucoside (QDG), quercetin-4′-monoglucoside (Q4G), quercetin-3-monoglucoside (Q3G), kaempferol (KMF) and myricetin (MRT) have been evaluated and compared with conventional solvent extraction. Microwave extraction offers important advantages like shorter extraction time (23 min), cleaner feature (no solvent or water used) and extraction of valuable onion crude juice retaining fresh organoleptic properties with higher phenolic content (58.29 mg GAE/g DW) at optimized power (500 W). Microwave extraction resulted significant yield (81.5%) with 41.9% of flavonol contents, with better retain of remaining flavonoids (55.9%) in residues of onions. QDG (239.7 mg/100 g DW) and Q4G (82.55 mg/100 g DW) have been reported the main flavonol in this study. Minor quantities of QA (traces), Q3G (4.22 mg/100 g DW) and KMF (3.99 mg/100 g DW) were also detected in microwave onion extracts.