<p>Flour modification is emerging as a vital strategy aimed at improving functionality, nutritional quality, and shelf life to meet the changing requirements of contemporary food systems. Traditional chemical and enzymatic modification methods, while effective, frequently face issues like processing duration, environmental impact, and limited sustainability. In this regard, microwave processing has surfaced as a quick, energy-efficient, and adaptable physical modification technique. This review thoroughly investigates the role of direct microwave and hybrid microwave-assisted treatments in altering flours sourced from cereals, millets, pulses, tubers, and unconventional plant origins. The focus of this review is on the fundamental mechanisms of microwave-matter interactions, especially the structural changes in starch, protein, and lipid fractions induced by dielectric heating. This review suggests that microwave treatment improves flour quality by enhancing functional, structural, and nutritional properties, thereby extending shelf-life. Furthermore, microwave-assisted techniques such as infrared heating, ultrasonication, and ohmic heating enhance process efficiency through synergistic effects, resulting in better product quality than microwave or conventional methods alone. Comparison and contrasts with traditional and innovative processing technologies are also presented to highlight the benefits and drawbacks of microwave-based methods. The implications of microwave-modified flours for product development, particularly in the realms of bakery, gluten-free, and functional foods, are also discussed. Ultimately, this review highlights significant knowledge gaps related to scaling up, process loopholes, and long-term stability and proposes future research areas to promote the industrial implementation of microwave-based flour modification within sustainable food processing systems.</p> Graphical Abstract <p></p>