Abstract The impact of gut microbiome composition was investigated at different stages of production (Wean, Mid-test, and Off-test) on meat quality and carcass composition traits of 1,123 three-way-crossbred pigs. Data were analyzed using linear mixed models which included the fixed effects of dam line, contemporary group and gender as well as the random effects of pen, animal and microbiome information at different stages. The contribution of the microbiome to all traits was prominent although it varied over time, increasing from weaning to Off-test for most traits. Microbiability estimates of carcass composition traits were greater compared to meat quality traits. Adding microbiome information did not affect the estimates of genomic heritability of meat quality traits but affected the estimates of carcass composition traits. High microbial correlations were found among different traits, particularly with traits related to fat deposition with decrease in genomic correlation up to 20% for loin weight and belly weight. Decrease in genomic heritabilities and genomic correlations with the inclusion of microbiome information suggested that genomic correlation was partially contributed by genetic similarity of microbiome composition.