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The microbiological monitoring of the fermentation process allows the detection and quantification of native yeasts and bacteria in order to avoid significant decreases in the ethanol yield and productivity. The use of antimicrobial agents reduces the damage caused by contaminants, but it is essential to determine which antimicrobial and dose are the most adequate for the rational application of these products. The choice of the microbiological monitoring method will depend on how easy it is to implement at the industrial unit. In this chapter, a small practical guide presents how to assess yeast and bacterial viability (direct counting and culture-dependent methods) and simple tests of bacterial susceptibility to antimicrobials, and provides the composition of culture media and solutions utilized in the methods to monitor the microbiological aspects of the fermentation process.