Breastmilk contains a complex community of bacteria that may help seed the infant gut microbiota. The composition and determinants of milk microbiota are poorly understood. Among 393 mother-infant dyads from the CHILD cohort, we found that milk microbiota at 3–4 months postpartum was dominated by inversely correlated Proteobacteria and Firmicutes, and exhibited discrete compositional patterns. Milk microbiota composition and diversity were associated with maternal factors (BMI, parity, and mode of delivery), breastfeeding practices, and other milk components in a sex-specific manner. Causal modeling identified mode of breastfeeding as a key determinant of milk microbiota composition. Specifically, providing pumped breastmilk was consistently associated with multiple microbiota parameters including enrichment of potential pathogens and depletion of bifidobacteria. Further, these data support the retrograde inoculation hypothesis, whereby the infant oral cavity impacts the milk microbiota. Collectively, these results identify features and determinants of human milk microbiota composition, with potential implications for infant health and development. Display omitted •Milk microbiota variability is affected by maternal factors and other milk components•Some factors have phylum-specific effects•Some variations in milk microbiota are sex-specific•Feeding method (at the breast versus pumped) was strongly associated with milk microbiota Moossavi et al. examine human milk microbiota in the CHILD birth cohort and use causal modeling to describe sex-specific associations with maternal, infant, and early-life factors. A strong association with feeding method (i.e., pumped versus directly at the breast) suggests some milk bacteria originate from the infant oral cavity.