Extracellular enzymes produced by predominant bacteria exert important roles in inducing and accelerating spoilage, with their secretion regulated by specific genes. In Pseudomonas fragi, the aprD gene is a recognized regulator for secreting an alkaline extracellular protease. However, limited studies have focused on this gene in P. fragi population and its impact on meat microbial community structure and function. This study addressed this gap by monitoring the changes in biological properties of P. fragi populations and analyzing the discrepancies in spoilage phenotypes and microbial community structures of chilled chicken among groups differentiated by the initial prevalence of aprD-positive strains. The results showed that aprD-positive strains were disseminated in P. fragi populations, and its prevalence was associated with significant increases in swimming motility and biofilm formation capacities in specific groups. In situ contamination experiments revealed varying spoilage characteristics and community compositions among groups by day 3 of storage. Correlation analysis demonstrated a strong association between spoilage phenotypes and certain bacterial genera, such as Pseudomonadaceae_Pseudomonas and Carnobacterium. However, the microbial community structure and spoilage characteristics of samples from each group were not significantly different on the 5th day of storage. These findings suggest that even a small number of aprD mutants can significantly affect the assembly of the chilled meat microbial community. Nonetheless, the regulatory effect of aprD on spoilage at the strain and population levels of P. fragi is negligible in the context of complex natural microbiota. This work underscores the complex interactions between specific bacterial genes and the broader microbial ecology in refrigerated meat environments, providing deeper insights into the meat spoilage mechanisms.