This study investigated changes in the microbial composition of microbrewed beer during the manufacturing processes and identified potential microbial hazards, effective critical quality control points, and potential contamination routes. Comprehensive quantitative (aerobic plate count, lactic acid bacteria, fungi, acetic acid bacteria, coliforms, and Bacillus cereus) and qualitative (Escherichia coli and eight foodborne pathogens) microbiological analyses were performed using samples of raw materials (malt and manufacturing water), semiprocessed products (saccharified wort, boiled wort, and samples taken during the fermentation and maturation process), and the final product obtained from three plants. The initial aerobic plate count and lactic acid bacteria counts in malt were 5.2 and 4.3 log CFU/g, respectively. These counts were reduced to undetectable levels by boiling but were present at 2.9 and 0.9 log CFU/ml in the final product. Fungi were initially present at 3.6 log CFU/g, although again, the microbes were eliminated by boiling; however, the level in the final product was 4.6 log CFU/ml. No E. coli or foodborne pathogens (except B. cereus) were detected. B. cereus was detected at all stages, although it was not present in the water or boiled wort (total detection rate = 16.4%). Results suggest that boiling of the wort is an effective microbial control measure, but careful management of raw materials and implementation of effective control measures after boiling are needed to prevent contamination of the product after the boiling step. The results of this study may constitute useful and comprehensive information regarding the microbiological quality of microbrewed beer.