Nowadays, the needs for understanding the biotransformation happening during the wine making process can benefit from the development of tools like flow cytometry. This powerful technique allows a quick and reliable detection and enumeration of microbial populations. Thus, by using the appropriate fluorescent dyes, specific probes and antibodies, flow cytometry can deliver information on metabolism and physiology of the cells or target proteins. Applications like the follow-up of alcoholic and malolactic fermentations as well as the detection of spoilage microorganisms are some examples of the potential of this technique. A large variety of kits can help the assessment of the viability and the vitality of microorganisms in wine. What is the future of such technology and what can we learn from the use of the flow cytometry in other application fields?