Coffee is among the most appreciated nonalcoholic drinks, and its consumption is distributed globally. Today, consumers can select their preferred type of beverage, from the most full bodied to the lightest flavors, organic or conventional, pale to dark, or with fruited flavors or with essences. e different types of coffee beverages depend not only on the botanical cultivar of the coffee bean but also on the different processing methods to which the fruits are subjected after harvest. e coffee bean used for beverage production is the endosperm of the fruit, often referred to as the green bean. To obtain the green bean, coffee fruits are subjected to either of the three different types of postharvest processing termed dry, wet, or semidry. e choice of process depends on the uniformity of fruit maturation, the local weather conditions at harvest time, and the availability of water at the production site. Each process, however, involves a stage of fermentation where the activities of microorganisms hydrolyze complex pulp-mucilage material of the fruit to help free the coffee bean. Although the characteristic flavor of coffee originates from the chemical composition of the bean, the microbiota responsible for the fermentation may also contribute to the beverage’s sensory characteristics and other qualities due to the excretion of metabolites produced during this process. e microbiology of coffee processing has been studied for about 100 years, but still remains as a traditional, relatively uncontrolled process conducted by the naturally occurring microbiota. is chapter describes the role of microorganisms in coffee processing. e previous reviews or discussions on this topic have been published by Arunga (1982), Jones and Jones (1984), and Schwan and Wheals (2003).