In this study, the effects of microwave treatment on hazelnuts artificially contaminated with aflatoxigenic fungi were evaluated qualitatively and quantitatively. The physical quality attributes (color, moisture loss, and sensory attributes) of microwave treated hazelnuts were also evaluated. A significant 3-log reduction in Aspergillus parasiticus contamination was observed after 120s treatment, no or similar changes were observed during the storage of microwave treated hazelnuts under the storage conditions. While taste and odour of microwaved in shell hazelnuts were unaffected during treatment and subsequent storage. microwave treatment duration of 120s was found to be capable of reducing fungal count of A. parasiticus on in-shell hazelnut without any noticeable change in nutritional and organoleptic properties of nuts. Based on this and the earlier study, a hybrid process is proposed, where UV-C surface treatment and vacuum assisted microwave are combined with air drying to increase the shelf life and control the quality.