The need for a reduction in the use of antibiotics in livestock to safeguard their efficacy requires the development of alternatives. In this line, the use of alternative by-products or ingredients, with functional properties brings the opportunity to improve pig health and thus, reduce medicalization. Therefore, in the present study, we aimed to evaluate the impact of an alternative feeding program based on unmedicalized diets formulated with fibrous by-products and functional feed ingredients on performance and fecal microbiota of young pigs compared to a common weaner diet supplemented with antibiotics. The alternative feeding program could anticipate the gut development of young piglets, which at the end of the nursery period presented a fecal microbiota more similar to that found in fattening animals. Moreover, piglets in the unmedicalized diets showed a trend to reduce the course of diarrhea immediately after weaning. The alternative feeding program showed, however, a reduced growth efficiency during the nursery period that needs to be discussed in the frame of the costs-benefits analysis of reducing antibiotics. This study aimed to assess the impact of two different feeding programs, including or not antimicrobials, on gut microbiota development at early ages in commercial pigs. For this, 21-day-old weaned piglets were distributed into 12 pens (6 replicates with 26 pigs each) and fed ad libitum until fattening with: standard commercial formula with antibiotics and zinc oxide (2400 ppm) (AB), and alternative unmedicated feed formula (UN). Subsequently, the animals were moved to the fattening unit (F) receiving a common diet. Pigs were weighed, and feed consumption and diarrhea scores registered. Feces were collected on days 9 (pre-starter), 40 (starter) and 72 (fattening) post-weaning and microbial DNA extracted for 16S rDNA sequencing. Piglets fed UN diets had a worse feed efficiency (p < 0.05) than AB during nursery; however, UN pigs spent less time scouring after weaning (p = 0.098). The structure of fecal community evolved with the age of the animals (p = 0.001), and diet also showed to have a role, particularly in the starter period when UN microbiomes clustered apart from AB, resembling the ecosystems found in the fattening animals. Fibrolytic genera (Fibrobacter, Butyrivibrio, Christellansellaceae) were enriched in UN piglets whereas Lactobacillus characterized AB piglets (adjusted p < 0.05). Overall, this alternative feeding program could anticipate the gut development of piglets despite a lower feed efficiency compared to standard medicalized programs.