Microorganisms have been harnessed to process raw plants into fermented foods. The adaptation to a variety of plant environments has resulted in a nearly inseparable association between the bacterial species and the plant with a characteristic chemical profile. Lactic acid bacteria, which are known for their ability to adapt to nutrient-rich niches, have altered their genomes to dominate specific habitats through gene loss or gain. Molecular biology approaches provide a deep insight into the evolutionary process in many bacteria and their adaptation to colonize the plant matrix. Knowledge of the adaptive characteristics of microorganisms facilitates an efficient use thereof in fermentation to achieve desired final product properties. With their ability to acidify the environment and degrade plant compounds enzymatically, bacteria can modify the textural and organoleptic properties of the product and increase the bioavailability of plant matrix components. This article describes selected microorganisms and their competitive survival and adaptation in fermented fruit and vegetable environments. Beneficial changes in the plant matrix caused by microbial activity and their beneficial potential for human health are discussed as well.