Paocai as a traditional side dish in Asia gains its popularity owing to the favorable tastes, which are bestowed by microbial metabolisms. The microorganisms involved in fermentation are mainly lactic acid bacteria and Saccharomyces, while low-quality Paocai may contain spoilage and potentially pathogenic microorganisms such as Escherichia coli. To monitor and control food safety for direct vat inoculation of Paocai, this study intended to develop propidium monoazide based quantitative PCR to enumerate fermentation starter Lactobacillus plantarum NCU116, as well as Saccharomyces and potentially present pathogenic bacteria. Universal and specific primers targeting different microorganisms were designed to identify and quantify total lactic acid bacteria, Lactobacillus plantarum, Saccharomyces, and Escherichia coli by establishment of standard curves, respectively. Plate counting was performed and showed comparable results to quantitative PCR analysis, indicating the applicability and efficiency of absolute quantitative PCR in fast detection of microbial composition in Paocai system. Nitrite as a hazardous substance in Paocai was also investigated by spectrophotometry and reverse transcription quantitative PCR. The mechanism of nitrite synthesis and degradation was studied, revealing nitrite reductase in lactic acid bacteria as an effective enzyme in reducing nitrite present in the fermented vegetable.