Infant formulas (IFs), the only adequate substitute to human milk, are complex matrices that require numerous ingredients and processing steps, which may impact protein digestion and subsequent amino acid absorption. The objective was to understand the impact of the protein ingredient quality within IFs on postprandial plasma amino acid (AA) profiles. Four isonitrogenous and isocaloric IFs were produced at a semi-industrial scale using whey proteins (WPs) from different origins (cheese vs. ideal whey) and denaturation levels (IFs-A/-B/-C), and caseins with different supramolecular organizations (IFs-C/-D). Ten Yucatan minipiglets (12- to 27-day-old) used as a human infant model, received each IF for 3 days according to a Williams Latin square, followed by a 2-day wash-out period. Jugular plasma was regularly sampled from 10 min preprandial to 4 h postprandial on the third day to measure free AAs, urea, insulin and glucose concentrations. Data were statistically analyzed using a mixed linear model with diet (IFs), time and gender as fixed factors and piglet as random factor. IFs made with cheese whey (IFs-A and -B) elicited significantly higher plasma total and essential AA concentrations than IFs made with ideal whey (IF-C and -D), regardless of the pre- and post-prandial times. Most of the differences observed postprandially were explained by AA homeostasis modifications. IFs based on cheese whey induced an increased plasma concentration of Thr due to both a higher Thr content in these IFs and a Thr limiting degrading capability in piglets. The use of non-micellar casein ingredient led to reduced plasma content of AA catabolism markers (IF-D vs. IF-C). Overall, our results highlight the importance of the protein ingredient quality (composition & structure) within IFs on the neonatal plasma AA profiles, which may impact further the infant protein metabolism.