Growing-up milks (GUM) are increasingly introduced into the diets of 1-3 years children in order to compensate the nutritional deficiencies which may occur in the transition phase of infant nutrition. In order to improve the GUM formulations, the aim of this work was to evaluate the impact of the GOS/FOS and the nature of the fat (vegetable oil (VO) vs milk bovine fat (MBF)) on the lipid and protein kinetics of digestion and on the minerals’ bioaccessibility of experimental GUM after in vitro static digestion. The GOS/FOS did not impact the overall degree of proteolysis and lypolysis. In opposite, faster intestinal protein digestion together with higher release of free fatty acids in gastric phase was found in the VO-GUM compared to the MBF-GUM. In accordance to the nature of the fat origin, different fatty acid profiles were found between samples. Higher calcium bioaccessibility was found in the MBF-GUM correlated to their lower palmitic fatty acid release. In addition, GOS/FOS may improve the bioaccessibility of calcium. In conclusion, the combined effect of MBF and GOS/FOS is the optimal ingredient association in order to have the best lipid profile and the highest calcium bioaccesibility.