In this review paper, several aspects of fruit juice microbiology, from past to future perspectives, are considered. An overview of the most relevant outbreaks involving foodborne pathogens and spoilage microorganisms associated with fruit juices is provided. One of the sections provides data on the sources of fruit juice contamination, followed by perspectives on preservation methods. Furthermore, considerations on the role of international guidelines about exotic fruit juices in respect to public health, and of the microbiological status of fruit juices used as food/beverage ingredients are discussed. Issues and challenges highlight how the microbiology of fruit juices has evolved over the years, when aspects of stability or microbiological safety are under consideration.