An ongoing challenge is to find alternatives to conventional cereals to feed livestock animals. In this study, common cereal grains were partially replaced by bakery (FFP-B) and confectionary (FFP-C) by-products in post‐weaning piglets’ diets. The aim was to investigate the effects of these alternative ingredients on faecal microbial population in the post‐weaning period. Thirty-six post‐weaning piglets were housed for 21 days in individual pens and fed three different diets: a standard wheat‐barley‐corn meal diet, a diet containing 30% FFP-B and a diet containing 30% FFP-C, for a partial replacement of conventional cereals. The faecal microbiota was characterized by the next generation sequencing of the 16S rRNA gene. No significant differences in the abundance, biodiversity and phylogenetic diversity of microbial population have been observed between groups. Both the unweighted and weighted beta diversities were not affected by the experimental diets compared to the control. Different bacteria as potential biomarkers between the three groups have been identified. Compared to the control, the inclusion of FFP-B increased the amount of Proteobacteria phylum, while FFP-C increased the amount of Firmicutes phylum. Given the limited effects on the gut microbiota composition and diversity, FFP-B and FFP-C can be potentially used as alternatives to cereal grains in post‐weaning piglets, but their effects on gut health need to be tested for a longer period and in different growth phases.