Infant growth trajectories reflect current health status and may predict future obesity and metabolic diseases. Human milk is tailored to support optimal infant growth. However, nutrient intake rather than milk composition more accurately predicts growth outcomes. Although the role of protein leverage in infant growth is unclear, protein intake is important for early infancy growth. This study of exclusively breastfeeding mothers with allergies (n = 161) from the Infant Fish Oil Supplementation Study assessed relationships between intake of human milk macronutrients and infant growth. Human milk fat, protein and lactose concentrations were measured at 3 months postpartum, and infant daily intakes were estimated using an average milk intake of 800 mL/day. Higher human milk protein:energy ratio was associated with higher weight-for-age z-score at 2.5 years compared to 3 months and higher body mass index-for-age z-score change (6 months to 1 year compared to 3-6 months). Maternal atopy and birth season (summer) were negatively associated with human milk lactose concentration. Passive smoke exposure was associated with reduced energy and fat concentrations and increased lactose:energy ratio. Our results indicate that intake of human milk macronutrients may impact early childhood growth.