Currently, the market for gluten-free products is experiencing a significant growth due to, mainly, the increase in the number of gluten-intolerant patients diagnosed and to the merging of a new niche market for consumers who optionally avoid gluten. Native flours are perceived as viable alternatives for industrially used starch and hydrocolloids blends, which lack in the vitamins and minerals that are in abundance in non-refined raw materials. This study delves into the potential of microwave technology in enhancing the functional and nutritional attributes of gluten-free breads. The research was conducted by employing 900 W microwave power for 8 min for buckwheat and teff flours modification with an initial moisture content of 30%. The modified flours were blended with rice flour and baked to verify the potential of microwave high moisture treatment for adjusting the texture and nutritional quality of the bread. The results revealed that microwave treatment of flours helped in retaining a higher level of essential nutrients and bioactive compounds in gluten-free breads.