Gochujang, fermented red pepper paste, is a grain-based Korean traditional food. The quality of gochujang produced by cottage industries is not well-documented. Thus, the present study aimed to analyze the quality of gochujang from 35 traditional cottage industries for physicochemical and microbial characteristics, along with volatile compound contents. In addition to microbial characteristics, salinity, pH, free amino nitrogen, and alcohol content were evaluated. Ethanol was detected as the predominant alcohol and 57% of tested gochujang products harbored >1% of total alcohol content, which was above the recommended level for halal products. Gochujang products contained hexadecanoic and linoleic acids predominantly and several volatile compounds belonging to the classes of alcohols, aldehydes, alkanes, nitrogen-containing compounds, and terpenes. A wide range of aerobic mesophilic bacteria (2.79–8.73 log CFU/g) and yeast counts (1.56–7.15 log CFU/g) was observed. Five distinct yeast species were identified, including Zygosaccharomyces rouxii. Eight gochujang products were found to be contaminated with Bacillus cereus (>4 log CFU/g). This study suggests that there is a need to limit B. cereus contamination in cottage industry products and reduce alcohol content to comply with halal food guidelines.