Vacuum microwave hydrodiffusion and gravity (VMHG), a modified form of solvent free microwave hydrodiffusion and gravity (MHG) technique, was used for extraction of onion by-products. A detailed study concerning about optimisation of different parameters like irradiation power, degree of vacuum and extraction time was performed. Subsequently, the temperature difference in different parts of matrix and also in the reactor was evaluated both in case of MHG and VMHG. Extracts obtained by VMHG, MHG and also conventional solvent extraction method (CSE) were analyzed for quantification of flavonoids by HPLC, along with studying the distribution of flavonoids in different intervals of time at optimised conditions. Two different methods were selected for evaluating the antioxidant capacity of these extracts along with determination of their phenolic content by the Folin–Ciocalteu method: the reduction of the stable DPPH (2,2-diphenyl-1-picrylhydrazyl) radical and the inhibition of the AAPH-induced peroxi-dation of linoleic acid in SDS micelles. Reduction of pressure up to 0.7 bar at microwave power of 500 W helped to increase the antioxidant activity of onion extracts with 57% increase in total quercetin contents against those obtained at atmospheric pressure. VMHG proved itself an efficient and environment-friendly technique allowing the extraction of flavonols at lower reactor temperature (81 °C ± 1), with improved alterations of tissues observed by microscopic studies, from onion by-products just in 26 ± 1 min, in the absence of any solvent.