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With ever-increasing health consciousness among consumers in the worldwide in the last decades, great attention has been paid on the application of biotechnology methods in the agricultural and food industry. Especially for plant-based foods production, which exhibit co-benefits to human the health and climate. Traditional fermented foods play a crucial role in human diets around the world because of their unique flavors, great nutritional value, and health-beneficial effects. Fermentation is one of the most traditional but still prevalent bio-processing approaches in the food industry, with the great potential to improve the flavor, sensory, nutritional value and biological activity (including antioxidant capacity, anti-cancer, anti-diabetic anti-inflammatory, regulating intestinal flora properties) of food products. The application of microbial food processing method has attracted the interest of researchers and industries due to its simple, environmentally friendly, and cost-efficiently advantages. The use of fermentation and selected generally recognized as safe (GRAS) starters, such as lactic acid bacteria, yeasts and filamentous fungi has been considered as an excellent method to improve the nutritional value or biological activity of foods by the biosynthesis/biotransformation/generation of bioactive compounds (e.g., phenolic compounds, oligosaccharide), or by the degradation of anti-nutritional factors. In the last years, the exploitation of microbes isolated from traditional fermented foods or as the result of the inoculation of selected starters was conducted to produce novel fermented plant-based foods with beneficial viable microorganisms and/or their metabolites that positively impact on human health. This Research Topic aims to focus on the application of microorganisms in processing of fermented plant-based foods to improve nutritional profile and/or biological activity. In particular, it is welcome focusing on matrices fermentation by beneficial microorganisms, processing for food substrate/by-product valorization, augmentation of food matrix bioactive compounds via fermentation. We invite authors to submit different types of manuscripts (e.g., Original Research Articles, short communications, and Review Articles) that focus on but are not limited to the following topics:  Microbial metabolic pathways associated with the accumulation of bioactive compounds of fermented foods.  Innovative fermentation approaches to improve the nutritional and functional properties in the final products.  Valorization of plant-based food matrices/by-products via fermentation.  Plant-based anti-nutritional factors degradation by microorganisms.  Development of high added-value and novel fermented products.  Production of bioactive compounds with health beneficial effects.  Human intestinal flora simulated effect on plant-based food.