Human milk (HM) influences infant feeding patterns and body composition (BC). This small proof-of concept longitudinal study investigated relationships between infant/maternal BC and HM casein, whey and total protein during the first 12 months of lactation. BC of breastfeeding dyads (n = 20) was measured at 2 (n = 15), 5 (n = 20), 9 (n = 19), and/or 12 (n = 18) months postpartum with ultrasound skinfolds (infants) and bioimpedance spectroscopy (infants/mothers). Proteins concentrations and 24-h milk intake were measured and calculated daily intakes (CDI) determined. Higher maternal weight, body mass index, fat-free mass, fat-free mass index, and fat mass index were associated with higher concentration of whey protein (p ≤ 0.034, n = 20). There were no associations between infant BC and concentrations of all proteins, and CDI of whey and total protein. Higher CDI of casein were associated with lower infant fat-free mass (p = 0.003, n = 18) and higher fat mass (p < 0.001), fat mass index (p = 0.001, n = 18), and % fat mass (p < 0.001, n = 18) measured with ultrasound skinfolds. These results show a differential effect of HM casein on development of infant BC during the first year of life, suggesting that there is a potential to improve outcome for the infant through interventions, such as continuation of breastfeeding during the first 12 months of life and beyond, which may facilitate favourable developmental programming that could reduce risk of non-communicable diseases later in life.