Recently, digestive efficiency (DE) was proposed as a trait of interest to improve feed efficiency (FE) in pigs, especially when they are fed with alternative feeding resources. Both are influenced by the host genetics, and also by the gut microbiota composition. The goal of this study was to quantify the impact of faecal microbial information on the prediction accuracies of genomic estimated breeding values (GEBVs) of FE and DE traits for pigs fed conventional or fiber diets. For DE traits, gains in prediction accuracy of GEBVs were increased by about 18% when microbial information was included in linear mixed models. In addition, these gains of prediction accuracy were very similar in both diets. For FE traits, no improvement was observed. Thus, the addition of microbial information in breeding programs is promising to better estimate GEBVs for DE traits.