Beer is a microbiologically stable beverage due to several inhibitory factors for microbial growth. In fact, only a restricted number of species can grow in and spoil beer. The vast majority of beer spoilage microorganisms are lactic acid bacteria belonging to the genera Lactobacillus and Pediococcus. However, many beer spoilage microorganisms exhibit extremely poor culturability, and they are hard to detect by the conventional laboratory media adopted for the quality control of beer. This often leads to quality incidents without the detection of the causative agents in breweries. In addition, the continual emergence of new beer spoilage species has been problematic for brewers that traditionally depend on species identification methods for quality control in the brewing processes. To overcome these difficulties, the brewing industry has strived to develop new microbiological media and species-independent methods for comprehensively detecting and identifying beer spoilage microorganisms. Some brewers are now evaluating new techniques, including inexpensive third-generation DNA sequencing, for the comprehensive identification of beer spoilage microorganisms and hygiene indicators. In this review, the recent progress of microbiological quality control methods in unpasteurized beer production is summarized.