Background Although there is intriguing evidence that breastfeeding (BF) and protein intake (PI) may influence contemporaneous nutritional status and long-term body composition, few studies have explored the nuances of these age-specific associations. Dietary and anthropometric data obtained from 3080 individuals from the Cebu (Philippines) Longitudinal Health and Nutrition birth cohort (1983-2005) were used to clarify the role of protein in influencing body size across the life course. Methodology We examined i) the influence of breastfeeding and PI on contemporaneous body mass index (BMI = kg/m2) from birth to 22y using random-effects longitudinal regression models, ii) whether age-specific PI from 2-22y relate differentially to later body composition (22y) using multivariable regression models, and iii) how longitudinal patterns of PI from 2-22y relate to young adult body composition using latent growth curve analyses and multivariable regression models. Results i) BF was associated with better nutritional status (higher BMI) in infancy and BF duration was inversely associated with BMI thereafter. Total complementary protein and complementary animal protein were positively associated with infant BMI Z-score (zBMI), while plant protein intake was inversely associated with infant zBMI. In post-infancy analyses, animal protein was associated with higher BMI. ii) Participants were classified into 4 mutually exclusive trajectories characterized by normal consumers, high consumers in infancy, usually-high consumers and always-high consumers. Compared to the normal consumers, always-high and usually-high consumers had lower predicted BMI, lean mass and fat mass at 22y. iii) Excess PI at age 2 was positively associated with BMI and lean mass at age 22y, while excess PI at ages 11, 15 and 22 were inversely associated with later lean mass, fat mass and BMI. Conclusion BF and PI significantly contribute to concurrent BMI across the life course. While age-specific PI and trajectories of PI were differentially related to later body composition, recent PI or PI pattern was most strongly related to adulthood outcomes. PI modifies risk of both current and long-term malnutrition. These findings support the optimization of early diets for promoting current and future health.