The aim of the present study was to evaluate a novel probiotic Pediococcus pentosaceus RC007 used alone and convined with Saccharomyces cerevisiae var. boulardii RC009, as in-feed additives to substitute the non-therapeutic use of antibiotics, and evaluate the different structural characteristics of intestinal bacterial populations between groups, correlated with pig production performance. The in vivo study was conducted on post-weaning pigs, from 21 to 56 days-old. Three dietary treatments were included: T1- basal diet (BD - Control group); T2- BD with P. pentosaceus RC007; and T3- BD with a mix of P. pentosaceus RC007 and S. boulardii RC009. The weight gain increase of pigs consuming non-therapeutic antibiotics was similar to those that did not consume antibiotics during the study (p=0.0234), but had better health indicators. The use of a probiotic combination increased carcass weight and significantly reduced the lumbar fat thickness. In terms of taxonomic composition, there was a tendency to modify the abundance of Proteobacteria, Cyanobacteria, Enterobacteriaceae and Lactobacillaceae in pigs that consumed the additives. The genus Butyricicoccus, Collinsella and Ruminococcus tended to be more abundant in the microbiota of pigs at T3. For the first time, the results of the present study indicate that P. pentosaceus RC007 and S. boulardii RC009, a probiotic combination, could be a good substitute for antibiotics in improving pig production performance, while also contributing to a healthier gut microbiota, especially with the reduced abundance of Proteobacteria and Cyanobacteria.