Short-term protein removal in vitro improves long-term blastocyst competence to survive vitrification. We investigated the mechanisms and effects underlying protein removal. Day-6 morulae and early blastocysts were cultured individually with and without protein for 24 h. Development and lipid content were analysed in expanded blastocysts derived from morulae (M-XB) and from early blastocysts (EB-XB). Expression of genes involved in lipid metabolism, stress responses and apoptosis was analysed in fresh and vitrified–warmed M-XB produced with and without protein. Pregnancy rates, birth rates and birthweight (BW) were recorded after transfer of embryos. Day-7 EB-XB production rates (with, 66.9 ± 6.2 and without, 68.8 ± 6.0 protein) were higher than M-XB rates (with, 21.4 ± 4.6 and without, 9.4 ± 4.6 protein; P < 0.005). EB-XB showed fewer lipids than M-XB (P = 0.03). In fresh M-XB, expression of sterol regulatory element binding protein (SREBP1) was lower with (4.1 ± 2.2) than without (13.6 ± 2.2) protein, contrary to results obtained for Patatin-like phospholipase domain containing 2, Hormone-sensitive lipase and Bcl-2–associated X protein (P < 0.05). Protein did not affect pregnancy rates and birth phenotypes (P > 0.05). However, BW was higher (P < 0.01) in calves born from vitrified M-XB (48.6 ± 3.4 kg) than from EB-XB (39.8 ± 2.9 kg). Such effects were more pronounced in females (P < 0.001). Calves from fresh embryos did not show BW differences. These results indicate that embryonic kinetics and vitrification impact birth phenotypes, at least in females. Alterations might involve exogenous protein and mobilisation of lipid stocks.