Introduction The salivary metabolome has been increasingly studied over the past ten years due to the potential of saliva as a non-invasive source of biomarkers. However, although saliva has been studied in relation to various diseases, its dynamic evolution during life is not known. This is particularly true for the first months of life. Infancy is indeed a critical period during which numerous behavioural and physiological events occur, such as dietary transitions and tooth eruption, which can lead to important biological modifications in the oral cavity. Objectives The aim of this work was therefore to study the evolution of the salivary metabolome during the first months of life by H-1 NMR. Methods Saliva of 32 infants with different milk feeding histories (breast vs formula) was collected at 6 stages, including 3 months old, 15 days before the onset of complementary feeding (CF), approximately 15 days after the onset of CF, approximately 21 days after the onset of CF and at approximately 11 and 15 months, and analysed. Results The longitudinal analysis showed a significant modification of the profiles of 18 metabolites over time; 14 presented an increase in abundance whereas 4 presented a decrease. These modifications seemed to be linked, for the most part, to an increase in oral microbial metabolism. Milk feeding history during the first months of life had no effect on metabolites. Conclusion This work shows that the salivary metabolome should be considered when studying the changes occurring during infancy.