Fermented plant-based foods have obtained growing interests for their improved nutrition profile, enhanced flavor and taste, as well as their health-promoting properties. Fermentation using lactic acid bacteria (LAB) and yeasts can eliminate antinutritional components and off-flavor compounds present in plant matrices while also generating beneficial metabolites. The interaction between fermentative microbes and plant substrates is dependent on plant matrices, microbial strains, and processing conditions. Accumulating evidence indicates that fermentation modifies the generation, degradation, and bioavailability of food bioactive compounds such as bioactive peptides, vitamins, volatiles, phenolics, phytic acid and phytates, saponins, and raffinose-family oligosaccharides. This chapter reviews and critically examines research data on microbial transformations of bioactive compounds in fermented plant matrices and pinpoints key factors contributing to inconsistent findings. It also identifies key research directions for understanding and applying fermentation-driven changes to improve the nutritional and functional quality of plant-based fermented foods.