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Extensive work has established the importance of the gut microbiota during the first years of life. However, there are few longitudinal studies describing the role of infants´ diet on the evolution of the fecal microbiota and their metabolic activity during this stage. The aim of this work was to explore the impact of diet on the composition of the major intestinal microorganisms and their main microbial metabolites from birth to 12 months. This is a longitudinal prospective study analyzing fecal microbiota, bacterial groups levels were determined by qPCR and short-chain fatty acids (SCFAs) levels by gas chromatography, as well as information from self-administered questionnaires about general characteristics and food frequency from a cohort of 83, Spanish and full-term, infants at 15, 90, 180 and 365 days of age. Results revealed that Enterobacteriaceae and Bifidobacterium decrease in weaning period contrary to Bacteroides group and Clostridium cluster IV. Furthermore, a clustering based on fecal bacterial groups, SCFAs and type of delivery and feeding, gender and living area suggested that the excretion of SCFAs is strongly related to the type of lactation. Conclusion: our study supports weaning period as a key step for gut microbiota transition and suggests the importance of the consumption of dietary fiber with the increase of certain bacterial groups as Clostridium cluster IV, which could be beneficial for the host. Finally, studies specially designed to analyze the production and the excretion of SCFAs in children are needed to understand how diet could influence in this process.