The duodenum is a key site of nutrient digestion and absorption in meat pigeons, and its microbial community may be associated with host body weight and breast muscle development. In this study, the duodenal microbiota of European meat pigeons and Shiqi pigeons at 14 and 28 days of age were analyzed using 16S rRNA gene sequencing. At 14 days of age, Firmicutes abundance was significantly higher in Shiqi pigeons than in European meat pigeons, whereas Proteobacteria showed the opposite pattern. Lactobacillus constituted the most abundant microbial group in both breeds. Spearman correlation analysis showed that Firmicutes and Lactobacillus were positively correlated with body weight and pectoral muscle percentage at 14 days of age, whereas Proteobacteria were negatively correlated with these traits. At 28 days of age, fewer between-breed differences in microbial community composition were detected; nevertheless, Firmicutes and Lactobacillus remained significantly positively correlated with body weight and pectoral muscle percentage in both breeds. These cross-sectional associations provide a preliminary reference for future studies of the duodenal microbiota and growth traits in meat pigeons.