Prepared dishes have high water content and complex nutritional composition, making them highly susceptible to microbial contamination and oxidative spoilage during storage. To elucidate the effects of microorganisms on the quality of prepared dishes and the formation of contaminants, the dishes "stewed pork with cabbage" were stored at 4 °C for 0, 1, 3, 5, and 7 days. Techniques such as high-performance liquid chromatography (HPLC), ion chromatography (IC), and 16S rRNA sequencing were used to explore changes in quality of the prepared dishes. The results showed that the total volatile basic nitrogen (TVB-N) and total viable count (TVC) consistently increased at similar rates during storage. The thiobarbituric acid reactive substances (TBARS) value reached 1 mg MDA/kg after 7 days of storage. Nitrite content and nitrate reductase activity rose as nitrate content decreased with longer storage. The contents of four free amino acids (FAAs) (Glu, His, Phe, Lys) and biogenic amines (BAs) (Putrescine, Histamine, Phenethylamine, Cadaverine) showed opposite trends. The abundance of the dominant genus, including Brochothrix, Acinetobacter and Weissella was significantly (P <
0.05) changed after the 3rd day of storage. Brochothrix, Acinetobacter, Pseudomonas, and Weissella promoted the decarboxylation of FAAs to form (BAs). Acinetobacter and Brochothrix accelerated the conversion of nitrate to nitrite. This study elucidates degradation of the quality of prepared dishes and the effect of five genera (Brochothrix, Acinetobacter, Pseudomonas, Weissella and Brochothrix) on the formation of nitrite and BAs, providing important theoretical support for enhancing nutritional quality and preserving the freshness during storage of prepared dishes.