This study evaluated production traits, apparent total tract digestibility (ATTD), and fecal microbiota composition in finishing boars (n = 207) selected for feed efficiency (FE; low = LFE; high = HFE) based on estimated breeding value for feed conversion ratio (FCR) within a Large White dam and sire genetic lines. Also, the association between gut microbiota with production and digestibility traits was investigated. Regardless of the genetic line, HFE pigs presented low FCR (P < 0.05), had thinner back fat (P < 0.05) and had greater loin depth (P < 0.05) than LFE pigs. Also, HFE pigs had a significantly higher ATTD for Ca and a tendency for a higher crude protein (P = 0.06) and phosphorous (P = 0.10) ATTD than LFE pigs. No significant differences in alpha- and beta-diversity measurements for fecal microbiota were seen between FE groups in each genetic line. The genera Lactobacillus and Prevotella were associated (P < 0.01) with some growth performance (e.g., feed intake), carcass traits (e.g., backfat thickness), and nutrient digestibility (e.g., Ca). In conclusion, HFE pigs had favourable production traits and higher digestibility of key nutrients than LFE pigs; however, the bacterial genera were associated with phenotypic traits but not by genetic merit.