Approximately one-in-ten reproductive age adults in the USA follow a plant-based diet, yet there is limited information on the influence of vegan and vegetarian diets on the mineral composition of breast milk. This study explored the major and trace mineral composition in breast milk and associations with maternal diet patterns. We used a cross-sectional design to collect a single sample of breast milk from individuals following vegan (n 23), vegetarian (n 19) and omnivore (n 21) diet patterns. Plant-based diet (n 42) was defined as following either vegan or vegetarian diets. Sixteen minerals were assessed using inductively coupled plasma mass spectrometry and inductively coupled plasma optical emission spectrometry. Data were evaluated using traditional statistical techniques and five different machine learning approaches. The distribution of Se (median; quartile 1 and 3) was significantly different between groups (vegetarians 21, 18–26 µg/l; vegans 19, 18–25 µg/l and omnivores 17, 14–20 µg/l; P = 0·007) using a Kruskal–Wallis test. Machine learning techniques also identified Se as a potential biomarker for differentiating breast milk by maternal diet pattern. Individuals following a plant-based diet generally had a lower BMI, higher breast milk Se and lower breast milk I and Fe concentrations compared with those following omnivore diets. This suggests that maternal dietary pattern (plant-based v. omnivore) may be helpful clinical information to consider when caring for the breast-feeding dyad, with the strongest evidence related to differences in Se concentration.